While it doesn't directly paint gay or effeminate men in a negative light, it also doesn't do enough to distance itself from the negative stigma men who don't follow traditional male roles face.
I think that non-nerdy people can't understand what it's really like to be nerdy. They attribute things to nerds (like acne or hubris) that aren't actually part of what a nerd really is. They just see a partial pattern and then paint the whole group with it.
Attempting to educate them about this doesn't really help, IMO. It's just extra stress, and so I try to just ignore their ignorance and go on my way.
Plus, I've noticed that kids these days put intelligence on a pedestal, and that's been awesome to see. The idea of a whole generation growing up and respecting people who can think well... I love it.