I absolutely think this is a bigger problem for women than it is for men, but I don't agree that it is exclusive to (or more prevalent in) "geek" culture. Pretty much any interest-based subculture that develops in an insular, mostly gender-exclusive way produces similar situations (think sports, or cars, or gambling, or fasion, or banking/finance, or comedy, or quilting, or whatever). In these sorts of groups, there is usually an archetypical picture people have in their heads of what a member will be like, and anyone who doesn't fit that archetype, for any reason, is going to receive increased scrutiny.
For a long time, "geek" culture was perceived to be mostly made up of men, mostly younger, and often socially outcast or stigmatized. Anyone who doesn't fit this mold perfectly will likely face some incredulity if they try to join in. Some of my best "geeky" friends from my younger days were hesitant to trust me at first, simply because they knew I liked to work on cars and had wrestled in high school. I didn't fit the archetype, and it took a long time for them to come around to the idea that I actually shared their interests and priorities. I don't think the attitude is born so much out of hostility as incredulity, it's just harder to believe certain types of people would want to be part of the group/subculture.
In the case of the "girl geek" reaction, I think this natural tendency is augmented by a few factors. First, I think most members of traditional "geek" culture have, at some point in their past, been victims of bullying or harassment, and have likely been made to pay for being too open or trusting with others. Second, gender has the unfortunate distinction of being one of the fundamental ways that people are classified, and as a result a gender "gap" between members is much harder to bridge or ignore than other kinds of differences. Finally, the fact that "geek" culture exists mostly online means that people are much more openly hostile and insulting than they would ever be in person. OK, I've probably gone on way too long already. Hopefully that makes sense?