If I had a dollar for every time I've seen someone going on about "believing in evolution", well … let's just say that I could afford quite a few hot dinners. Despite being well-fed, however, I'd still be grumpy about the lack of understanding about how "believe" differs from "believe in".
It is probably a largely semantic issue - what do we really mean by believe?
For me, a belief is related simply to the state of considering something to be true. I believe that I am sitting on a chair (in part because I am sitting on a chair). For a theist (the sort of person most likely to err and say that others "believe in evolution") belief can mean something more, so that it involves an act of will, perhaps even the overcoming of doubt (often caused by evidence that shows that supports the notion that a specific belief is false).
Sometimes an atheist like myself will use "believe" in a slightly different way, so as to imply doubt - not doubt that has been overcome, but doubt that remains. So I might say that I believe my football team will win on the weekend, because I don't know that they will and I'm a little more confident that I would be if I just said that I hope that they will win. But I am nevertheless aware that there's an element of hope in there - you know, like wishful thinking.
I think that this can lead us atheists, at times, to misconstrue how a theist thinks about belief. We tend to see this form of belief as lying a lot closer to hoping (or dreading if we are less optimistic) while I think that theists see it as being a lot closer to knowing (perhaps some theist or ex-theist could shed light on this). If so, then there's an element of magical thinking, similar to those life-coaches who rattle off such nonsense as "if you truly believe it, it will come true".
"Believing in" something is quite a different concept to "believing" it. Say I was listening to the coach of my football team as he described how the team planned to make the finals next season, that they've all been working very hard, making sacrifices and putting the "I" in "team". To say that I don't "believe" the coach is to say that I think he's lying - they haven't been working hard enough, not enough sacrifices have been made and there's no "I" in "team". To say that I don't "believe in" the coach is to say one of (at least) three things.
Firstly, I could be saying that I don't have any confidence in him, that I don't think his plans are sufficient to get my team through next season or something like that.
Secondly, I could be implying that I don't think that the idea of coaching is a good one, suggesting that it would be better if all the members of the team just did their own thing and turned up on the day and tried their best (an approach which I heartily recommend to all competitors in the league).
Alternatively, I could be saying that I don't believe that he exists. This would of course be ridiculous, he's right there, giving a speech that I am listening to. It would of course be quite different if I didn't believe in the coach that you were listening to, if I could neither hear nor see him.
If we talk about "believing in evolution" then strictly speaking, we know it happens - because we breed dogs, and cats, and sheep, and pigeons ... we can force them to evolve. Not even a creationist could argue against that (well ... a somewhat mythical beast, the rational creationist, couldn't argue against that). The sort people making the claim along the lines of "atheists believe in evolution" are actually referring to the theory of evolution. Does the theory of evolution exist? Well, yes, it does. No-one is contesting that, as far as I know, not even the creationists.
We could ask a similar question: "do atheists believe in creationism?" Strictly speaking, we do, because creationism exists. We sort of wish it didn't because it rots people's minds, but wishing something doesn't make it true.
Then there are the other meanings of "believe in".
Do we "believe in" natural evolution meaning that we think it is a good idea? Well, no, I don’t think so. Instead, we tend to avoid it. After all, we don't look on dispassionately as our children fail to evolve quickly enough to counter the latest version of the influenza virus. We don't let women die in childbirth because their hips aren't wide enough. We don't let myopic people die out (imagine making them drive without glasses for the sake of evolution …)
Or do we have confidence in evolution, in the same way as we might have confidence in and thus believe in the coach? Since evolution is not goal oriented, this doesn't really seem applicable. There might be some people who have some bizarre faith that, if we don't come to grips with climate change, everything will be alright because we'll just evolve gills. Such people don't comprehend how evolution tends to viciously prune its metaphorical tree of failed experiments, something like 99.9% of all species that have ever existed are now extinct (being aware that species are designated by humans, really there are only as many species as we are collectively aware of, so this estimate is based on some rather rubbery assumptions). If humans manage to be part of screwing the environment up so badly that we can't live in it, we won't magically adapt - we'll just die out, like most of the dinosaurs did as the Earth's climate changed on them over a period of 175 million years.
So, we don't believe that evolution is necessarily good, nor that it necessarily aligns with our goat of ongoing survival as a species. Therefore, we don't "believe in" evolution in either of those senses.
But, given careful definitions of the terms "believe", "evolution" and "is true", almost every single one of us does believe that evolution is true.