It's been said above, but I'll echo it again.
Gaming was a fringe enthusiast hobby and a refuge for certain types of people - mostly boys, but there were girls as well - while growing up. I was with a group of friends who happened to like games, and we were bullied for it. It wasn't just physical, there were times when it was verbal, and times when it was done by women. In certain situations there was nothing worse than being emasculated by a woman in front of a crowd, and that happened to me and several of my friends. Of course, I got over it as did my friends, and none of us blame women or are angry at them for that. Not even the ones that did it to us. It's better to forgive and forget, but sometimes that's not always possible.
I think there are remnants of that in the gaming community. I think it's a societal issue related to gender, and it permeates everywhere, not just gaming.
It's also propagated by culture and marketing. I mean some marketing for some products makes misogyny in gaming practically childs play. That Dr.Pepper "Not for Women" commercial comes to mind.
Then there is the fact that gaming has become mainstream seemingly overnight. This is the part where I reach out to other people in the thread and declare my own age. I'm 25. When I was finishing high school I think that was the time Assassins Creed first came out. The landscape was just VERY different back then. Like, sometime during my time at Uni it became acceptable, and it was just another thing. Does that seem familiar to anyone? I'm not the only who got that vibe, right? That's why #GamerGate was something I thought was important. It may be silly to call yourself a gamer. Gamer may be a silly term, but it's a thing now. When I went to meet and greets/date nights whatever at Uni you'd meet lots of people and give them the cliffnotes of your hobbies and such. I play videogames. It's a hobby just like running, golfing, playing guitar, and reading. It's not a big deal, but as soon as I mention that I play games, I get called a gamer. It just happens.
But with that said, I think such a culture shock tend to bring with it change. And I think this change was rapid. And let's face it, not all gamers are socially well adjusted individuals.
Thing is though, that's not stopping women. If gamergate taught me anything it's that there are seemingly tons of women out there in gaming, and they love AAA games. I dunno, maybe that's just the small lens I've been looking through. But I think it's not something to dismiss out of hand, either. Like Guppy said, the issues in the gaming community are very insular due to the nature in which they are confined. That is to say, websites and forums such as Kotaku, Reddit, 4chan, Something Awful, and here. Most people don't bother themselves with it, and remain oblivious.
It's just a small group of assholes being assholes. This is a people problem. Theres always going to be a % of assholes in a group. As the sample size increases the raw number of assholes gets larger.