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.