Let's imagine a ridiculous situation - suddenly, some town somewhere makes it mandatory that each class day begin with a communal prayer. All students must recite this prayer. For fun, let's make it Catholic - the Hail Mary.
Would the protestants have reason to be upset? Sure they would, since (at least for most protestants - maybe there are some exceptions) a prayer asking Mary to pray for us would violate their beliefs.
Muslims? Absolutely, for similar reasons.
Atheists? The instinctual response, I think, is 'absolutely' - along the same lines as the muslim or the protestant. But I don't think this works at all. In fact, at least insofar as we're considering the atheist as an atheist, the answer seems to be 'not at all'. If the atheist is going to have reason to complain, it's not going to be owing to being an atheist.
After all, atheism is pretty thin on belief content. If we play the game where atheism is the mere lack of a belief, then clearly 'lack of a belief' isn't going to motivate one to be offended by or unwilling to partake in a prayer. At worst, it's some kind of busywork.
Let's go with the stronger, and more accurate definition of atheism: belief that God does not exist. Okay, that's sturdier. But it still doesn't help. So they believe God doesn't exist - that isn't enough to make reciting a prayer noxious or offensive. Pointless, perhaps. Or maybe not. It could even be something they enjoy. Maybe they'll find the idea conveyed in the prayer beautiful even if they don't think it's "doing anything" or reaching anyone.
But the atheist, as an atheist, doesn't seem to have reason to complain. Maybe not even legal standing.
Now, that's not to say you couldn't come up with an atheist who would argue, properly, that the prayer is offensive to them. Say, they have a belief that prayers are stupid or... etc, etc, and that belief is being violated. But it seems to me it would actually have to be a lot more developed than merely "I'm an atheist!" or even "I'm a naturalist!" What would be necessary is an appeal to some kind of belief system they subscribe to - or, I suppose, something merely emotional. "I don't like praying, and that's that!"
I don't have some major aim or goal with pointing this out. It's interesting to note the situation, which I think can be parleyed further - an atheist as an atheist wouldn't necessarily have a problem even with a full-blown theocracy. In principle, they may even be in favor of one. Actually, I'd love to see an atheist complainant defending their complaint in a court of law. It's easy to picture the muslim appealing to their religious beliefs, the protestant appealing to his religious beliefs. The atheist? I could just picture the lawyer inquiring as to just what religious beliefs of theirs were being offended. What the violation of conscience was in the case of an atheist compelled to pray. I'm sure they could give one, but seeing it justified in that context would just have some potential for fun.