Here's the thing. Atheism is not (or at least not always) an active denial of the existence of god(s); rather, it's a lack of belief that god(s) do exist. Atheism has no holy book, no doctrines, no dogmas or anything like that. There is literally no way in which atheism as a whole can cause or justify anything, just like not believing in santa can cause anything. Of course, this doesn't mean that an atheist is magically incapable of violence or otherwise discriminating against others, but that's not because of atheism but rather because of either simple human nature or because of something that goes beyond basic atheism.

As for communism: Communism =/= Atheism. Communism is a political/economical/social system with the intent of creating a classless, stateless community. Everyone would be equal regardless of their job or skin colour, there would be no elite class. There would be no poverty by virtue of everyone getting what they need as long as they give what they can give.
Honestly, on paper (Note that I said on paper, I know that in practice it doesn't work) it's pretty much the best system there is, IMO. However, the problem lies with human nature not being happy with being equal to everyone else. We always strive to be better than the rest, earn more than the rest and whatnot. This generally results in the leaders being corrupt jerks who have all the resources and everyone else being left in the cold, and woe to anyone who tries to protest to the system -- something which we can see in just about every single other system ever, by the way.