Is the question just about atheists specifically, or about nonbelievers in religion generally? Some of the comments seem like a backhander at atheists specifically. What I will say is that people who make unflattering comments and generalisations about nonreligious people don't distinguish between atheists, agnostics, or any other variant of religious nonbelievers. If you're not religious they think you're one of the disreputable, whatever you might call yourself.
People fear what they don't understand and religious people don't care about understanding because it's too much work to have to think for yourself. Also, some people view us as Satanists or the Anti-Christ, which I guess we are pretty much the latter one.
I think they hate people who don't fit into thier perception of the world which for some religions are non believers. I don't think athiests are evil but as we do not like theists forcing beliefs on us we shouldnt either. If you regect someones beliefs they think you are rejecting them personally what ever that belief is religious political ecetera..
Atheists are unbelieving in god, not nice. Many are nice, some are not.
Anyway, people hate atheists in large measure because they have no fucking clue what atheists are and aren't and what the actual implications of atheism are and aren't. They simply believe the stereotypes and lies they are taught. Also, they are controlling assholes and there's nothing they care more about controlling than someone who blasphemes the central tenets of their belief-system.