Don't atheists have faith in science just like religious people have faith in God?

In a sense, that is correct, but only in a very simplistic sense. Religious people who make this argument would do well to heed their own counter-arguments when we atheists say that faith is not a virtue. One of the ways religious people respond to that criticism is to say that "faith" doesn't necessarily mean "blind faith;" it can also mean "justified faith" (as in, "I have faith that Steve is a loyal friend because he's proven his loyalty over and over again"). Blind faith is believing something without any meaningful evidence, whereas justified faith is being convinced of something because of evidence, but recognizing that due to the problem of induction, you can never be 100% sure that there isn't some further compelling evidence in the other direction that you just aren't aware of. I think we can have justified faith in the scientific method and the scientific community.

In my case, I did a lot of personally examining the evidence in favor of evolution; I was actually so indoctrinated by creationism that I continued to believe evolution was dumb even after I stopped being a Christian. But then eventually I decided that I should look into the evolutionist rebuttals to creationist claims, and I found the rebuttals to be far more convincing, and backed up by far more evidence. And whereas creationists claimed that evolutionists were just dishonestly propagating a science they knew was false to validate a specific worldview, the creationists were the ones who openly acknowledged that they would simply ignore or discard any evidence which goes against the conclusions they already had going in.

Bottom line, my examination of the evolution issue was pretty thorough and in-depth, and I don't really think I believe in evolution based on faith (even justified faith) in the scientific community. Yes, there are always things that we don't experience firsthand, but there has to be a limit of reasonable skepticism to what information we doubt just because we didn't experience it firsthand (analogy: somebody doubts that a certain law was passed, and you show them the text of the law straight from congress.gov, but that doesn't convince them because hackers could've just planted false information on the official government website; yes, it is technically possible, but it's outside the realm of reasonable likelihood). If a person is going to be that skeptical and that demanding of firsthand experiential information, then I would fully expect that they're only applying that extreme level of skepticism to worldviews they disagree with, because there's no way their own beliefs would hold up to the same demand (unless, perhaps, their own worldview is full-blown solipsism).

Anyway, bit of a tangent. The point is that I have investigated evolution myself quite thoroughly, and found the position of mainstream science to have far more hard evidence to support it. So then, when people attack the position of mainstream science on issues like climate change or vaccinations, I see a lot of similarities between their lines of attack on those issues and creationism. I haven't done a tenth of the research about climate change that I've done about evolution, so yes, I do have some degree of "faith" in the scientific community on that issue, but it's faith that is justified by my more in-depth examination of how science gets the job done on the issue of evolution (and some other minor issues that were quicker and easier to research).

So that's the main way that I would respond to this criticism, but there is one other small point worth mentioning. I think another way our "faith" in science is different from the religious faith that many believers have is that it's subject to change in light of new information. There are many religious people who actually take pride in the fact that their beliefs wouldn't change no matter what new information came to light (like William Lane Craig saying that the ultimate evidence which supersedes everything else is "the self-authenticating witness of the Holy Spirit," i.e. a gut feeling). But the thing about having some degree of trust in the scientific community is that you recognize it's just humans doing the best they can, not some divine word from on high, so I think that makes it much easier to be humble and accept that we should be open to new information potentially changing our position, instead of blindly walking in lock-step with whatever mainstream scientists believe at the time. But I do think that once you've done enough research for yourself to see that mainstream science isn't just some shadowy cabal of people trying to foist a specific conclusion on the unsuspecting public to support some selfish worldview, then it does make sense to take an "innocent until proven guilty" approach to the mainstream scientific consensus on an issue. Because, as others have said, it works; it gets results.

Isn’t it meaningful that all the disciples died for their beliefs?

William Lane Craig (one of the most passionate defenders of the resurrection as a historical event) and many other Christian apologists use this argument from martyrdom with stubborn regularity. It makes sense to some degree, because if it is true, it’s a very powerful argument for a transformative experience outside of themselves. But there are two problems with this argument. The first one is pretty huge; there’s no real solid evidence I could find that any of the disciples did die for their beliefs at all. And it’s not just because I was only looking at skeptical sources; even the Christian websites I found couldn’t come up with anything better than “second-century church tradition.” The lack of historicity for this claim should be made clear by the fact that Craig himself (who’s fond of using arguments from authority to bolster his claims) doesn’t even try to back this one up with a quote from a scholar or a blanket statement of scholarly consensus. Generally, the only specific evidence he cites for this claim is a passage in Josephus about James, as seen here:

According to the first century Jewish historian Josephus, James was martyred for his faith in Christ in the late AD 60s. Now most of us have brothers. What would it take to convince you that your brother is the Lord, such that you would be ready to die for that belief? Can there be any doubt that this remarkable transformation in Jesus’ younger brother took place because, in Paul’s words, “then he appeared to James”?

Even in a written piece like this (which doesn’t have the time restrictions of formal debates), Craig can only provide any actual citation for a single one of those many disciples who supposedly went to their deaths refusing to deny their belief in the risen Lord. As far as I’ve ever seen, there is no historical evidence that most of the disciples were martyred, prior to second-century church tradition. And yet, Christian apologists keep right on stating this as fact, without bothering to ever produce any sources that can validate such a high level of confidence in its historical accuracy (seemingly, because they don’t actually have any). That seems intellectually dishonest to me.

Now, I think that in itself should be enough to cast serious doubt on this point, but there is a second factor that needs to be considered. Even if some of the disciples were killed, it only has significance to the strength of their belief if they were killed after being given a chance to recant. If someone puts a gun to your head and says, “admit you were lying or I’ll kill you,” and you stick to your story, then that’s pretty strong evidence that you really believe it. But if you’re walking down the street, and someone just shoots you without making any such challenge, then it says absolutely nothing about whether you really believed whatever it was you were claiming. So, for this claim (that the disciples went to their deaths unwilling to recant) to be substantiated, there has to be historical evidence not only that they were killed, but also that it only happened after they were given a chance to recant. Now, let’s look at the passage from Josephus about James that William Lane Craig offered as such profound evidence for this argument. It fails that criterion on both levels. It does not indicate that James was given a chance to recant his belief that Jesus rose before he was executed, and it doesn’t even indicate that this belief was why he was executed in the first place. Contrary to how Craig describes it, there is no indication in Josephus that “James was martyred for his faith in Christ,” or that he specifically did “die for that belief.” It’s actually remarkably vague about the reasons for his execution, which makes it easy to read between the lines that his seditious faith in Jesus as his savior was the real reason, but only if you already believed that going in. Assumption is not evidence.

In my perception, the passage about James in Josephus is the most oft-cited evidence of martyrdom by one of the disciples who allegedly saw the risen Christ, and yet this is how thin it is. It’s like saying that someone who claimed to be an alien abductee was killed in a mugging, so that must mean he really believed he was abducted. It’s an argument that sounds very dramatic and compelling at first blush, but doesn’t hold up when you actually look closer at what evidence the proponents of this argument are citing to substantiate their claim.

Have you ever actually read any of William Lane Craig's books?

The short answer is no, not any of his whole books. The long answer is, after seeing a lot of arguments from him in other forms (he even answered a question from me in his Q&A column), I don't believe it would be anything but a complete waste of time to read a whole book. Observe the following quote…

First of all, I think that I would tell them that they need to understand the proper relationship between faith and reason. And my view here is, that the way in which I know Christianity is true is first and foremost on the basis of the witness of the Holy Spirit, in my heart. And that this gives me a self-authenticating means of knowing that Christianity is true, wholly apart from the evidence. And, therefore, if in some historically-contingent circumstances, the evidence that I have available to me should turn against Christianity, I don’t think that that controverts the witness of the Holy Spirit. In such a situation, I should regard that as simply a result of the contingent circumstances that I’m in, and that if I were to pursue this with due diligence and with time, I would discover that in fact the evidence, if I could get the correct picture, would support exactly what the witness of the Holy Spirit tells me. (Source)

…And by the way, that’s not just something he said in an interview in the spur of a moment. I did research his actual scholarly work enough to know that his flagship book (Reasonable Faith) has a whole section on this, where he repeatedly reinforces the idea that the way Christians know Christianity is true is ultimately because of the self-authenticating witness of the Holy Spirit, so reason and rationality must only ever be subordinate to that.

See here (Google Books link is dead, but you can follow along if you happen to have a physical copy), the section starting on page 47 with the header “Role of Argument and Evidence.” Here are a few of the most damning quotes, if you don’t feel like reading the whole thing…

“I’ve already said that it is the self-authenticating witness of the Holy Spirit that gives us the fundamental knowledge of Christianity’s truth. Therefore, the only role left for argument and evidence to play is a subsidiary role.” 

“Reason is a tool to help us better understand and defend our faith;” [...That is, not to find out whether our faith is actually true or not.]

[Down on page 51] “Therefore, the role of rational argumentation in knowing Christianity to be true is the role of a servant. A person knows Christianity is true because the Holy Spirit tells him it is true, and while argument and evidence can be used to support this conclusion, they cannot legitimately overrule it.”

…In short, Craig admits over and over again that his entire worldview is based on a feeling, not facts, data, arguments, or evidence. He further admits that no amount of arguments or evidence would ever changes his mind, and even seems proud of that! He then compounds the sophistry of ignoring arguments himself while using arguments to convince other people, by reframing the feeling which serves as the basis for his belief in an intellectual-sounding buzz-phrase, “the self-authenticating witness of the Holy Spirit.” At the end of the day, he’s no different from all the Young-Earth Creationists who openly admit that they will simply dismiss any evidence which goes against their presuppositions. He’s not a bit different. But I’m supposed to respect his intellectual or philosophical acumen?

But wait there’s more; there’s also this other little nugget which he wrote right above that section on page 47…

“Therefore, when a person refuses to come to Christ, it is never just because of lack of evidence or because of intellectual difficulties: at root, he refuses to come because he willingly ignores and rejects the drawing of God’s Spirit on his heart. No one in the final analysis really fails to become a Christian because of lack of arguments; he fails to become a Christian because he loves darkness rather than light and wants nothing to do with God.”

…I don’t know about anybody else, but I know (just as fully and confidently as I know anything about myself) that the reason I’m not a Christian has nothing to do with loving darkness rather than light. But hey, William Lane Craig is the foremost Christian philosopher of our time, so he must know my own heart, my own motivations, better than I do, right? Pardon me if I’m skeptical.

So, just that quickly, in one short section of one of his thirty or so books, he’s completely torpedoed his intellectual credibility for me in not one, but two different ways. And that’s without even factoring in all the many things he’s said and done to torpedo his credibility for me in all of his many debates.