I don't know about TV in general, but the top-notch shows usually don't misrepresent atheists. I'm thinking of Star Trek, Stargate, The West Wing (although they're underrepresented, it's the nature of American politics so it's no surprise, there), etc.
I think part of the issue is a sort of bias in terms of the nature of atheism itself - a normal atheist generally doesn't make a big deal about their atheism, whereas the bad ones tend to be far more vocal. While this reasoning also applies to religions (the bad ones tend to be the most vocal), there's no way for an atheist to show their atheism through their actions, in the way that religious people can (through prayer, etc). So what ends up happening is that normal atheists in a lot of TV shows don't really register as atheists because it's irrelevant to the storyline and normal atheists don't make a big deal about their atheism. Meanwhile, the bad atheists tend to have their atheism as a major part of their personality, so it produces a net negative image, not because of misrepresentation, but because of the way things are.
Having said all this, I wouldn't be surprised if some shows intentionally misrepresent atheists, especially American shows.
(EDIT: Apologies if others have already made these points, I don't really have time to read through every post right now, just wanted to post my opinion)
