'These aren't the cuddly nerds we made movies about in the '80s.'
-AARON SORKIN, screenwriter of The Social Network, acknowledging that the film, which purportedly tells the story of Facebook's founding, is sexist toward women because he was trying to depict a "deeply mysogynistic group of people" (Verbatim in TIME, 2010.11.08)
I've mentioned this before in relation with gamer geeks, but I've also spent a lot of time with computer and "Ănĭme" geeks and found that they tend to be just as bad. For the former two, I imagine that comes from the fact that they're vastly straight-male-dominated communities, and the few ladies presumably feel the need to conform to fit in. The latter may have something to do with the objectification of the female form in the medium. (There's, of course, also the fact that most media reflect general society's stereotype that masculinity is the default, on which I'll hopefully expound in a post of its own.)
All of these also have the contributing factor that they're counterculture and thus include a lot of people who don't spend much time in mainstream society where they have to have social skills. On the other hand, I can't say from my experience that "normal" people are any better. Everywhere I've ever been in my life, I've seen that society is ruled by male bullies. Even in terms of how we select partners, ladies have been for millennia trained to be attracted to the most violent, vicious men, as these are the ones who fulfill their rôles and provide the best.
From all this, you can see one of the reasons why I have so few friends, and they the ones who are, at least to some degree, the exception that proves the rule.
So why do we have these highly fictionalized "nice guy" nerds in film and television? Maybe it has to do with writers and directors being on the geeky side themselves.