I'd hesitate to say "geek culture" went mainstream so much as geek hobbies did. A geek was once defined to me as someone that takes to extremes what someone else does in moderation, and in that regard, we're still marginalized. We happily research our hobbies while others see looking up wikipedia as too much work. WE like a movie based on something, we try the source material, while the Dark Knight didn't move Batman comics to new readers. We get weird looks for devoting time into a video game to 100% it. Heck, several of my family openly state they won't read a book longer than 300 pages (the crap I read gives them a heart attack. I haven't read a book that short not first published in Japan in years). We watched the subtitles. We modded the game. We enjoyed something before ti was popular. When some of that gets practiced by more people I'll surrender we won, but for now, people only like things like the Avengers if they can be consumed in small sedentary bites. One of these geek movies will flop if it hinges on something even as simple as having to go in having read a free online comic.
Moreover there's something to consider. Most of our persecution was that call to conformity, and we didn't just get it from bullies. Parents, teachers, even friends all tried to move us into paths they thought we should take with differing levels of success. While there's always an online pissing contest about what is better than what, most of the time in public we were well behaved and accepting that we all like differing things, and that the world can actually get along without having to try and invalidate someone else's likes. I have to believe at our core that is a geek philosophy, or else we'd have seen a blood bath at some convention over a Star Wars versus Star Trek debate.
Then the activists get involved.
I honestly have little to no trouble if harassment was what these guys dominantly went after, but it seems that more and more they're attacking content for not being 100 percent sanitary to their beliefs. Hey, a game is coming out with character with impossible breasts, I must squash it because I apparently can't just let it be. I have to condemn it for not appealing to me and make anyone that isn't similarly offended or *gasp* likes it is shamed into my line of thinking. The realm of geekdom is limited by our imaginations and willingness to look outside the mainstream outlets, so I reallly do wonder why some people feel that things they don't like seem to have so little allowance to exist. I get they can be overdone, but no one seems to put numbers on these things to prove that this is the case, nor are they adding new plot ideas or characterizations to the table. I know many mean well, but somethings I flash back to high school endlessly being told I'm not allowed to like what I like, I must like what someone else does.
And that's not getting into oversensitivity. There in many ways is how geekdom hasn't spread out. We had to let a lot of harassment and insults roll off our back. We never liked them, but crying to the principal never seemed to do much. Over time, we started wearing the insults of nerd, geek, or otaku as a badge of honor and it didn't seem to hurt us. Today guys get fired over a bad joke about a dongle. You can't criticize any of these ism groups without somehow being against everything they stand for. The wrong word or phrase can net you nothing but trouble. And why? Because some believe that people should never be treated poorly ever. If one bad joke might lead to some hurt feelings it must be killed and the one that made it be made an example out of, and unlike us, they get away with it. I won't deny some bitterness about that, but I think, again, long term geeks have to come to terms about not having the right to not be offended. A lot of our favorite works, from the Dark Knight Returns, to something like Mystery Science Theater wouldn't exist with concern for hurt feelings, and the recent PC police will just further stifle creativity as people afraid for their jobs keep everything safe.
I'm not saying we can't do better, but the people that seem to complain we're excluding them only seem to say so because we aren't bending over backwards to their vision of the world. Treating people with respect is one thing, and big problems in that area need to be addressed. But if people act like everything should be tailor made and sanatized for their protection, you can't be surprised when those people aren't welcomed with open arms. at best it sends us back to the days of being told what we must like. At worst, it's a sign of laziness that in the world where creativity is fairly easy (thanks to the internet) you'd rather complain and make others do the work instead of building on your own.
Both are signs that many of the things that made us geeks didn't cross over.