Considering I've never been much part of any other subculture (and even saying I'm "part of the geek culture" is stretching it), I can't say how much this is a problem in, say, wrestling or sports fandoms, but IMO the core of the problem is this:
Nerd culture is a culture that thrives on passion. Collect more comics, more video games, more merchandise. Look, have you got this super exclusive 25th anniversary 7-disc bluray of that one movie you like? Get that too! Have you been to E3 this year? What about Gamescom, PAX, Quakecon etc.? The more passionate the fans, the more lucrative the business will be, as more media, merchandise and stuff can be marketed for them. It's a seemingly win-win situation: geeks get more of what they want, and businesses thrive. But this passion has a dark side, and its name is fanboyism. In a world of forums, user groups, subreddits and other closed groups of like-minded individuals it's easy to find oneself in an echo chamber. A place where everyone agrees with everyone within that particular system, and feeds each others' beliefs that yes, Nintendo IS indeed the best at everything, that Marvel IS indeed the absolute pinnacle of comic books movies from here to eternity, video games ARE in fact the highest form of art and so on. When this bubble bursts, or the individual steps out of the echo chamber, full of confidence in that their stances and beliefs are right, the feeling when someone calls Nintendo a pile of hacks recycling the same formula for decades on end can provoke a senseless reaction, leading to ad hominems, harassment, twitter feuds and other petty shit. Hence why so many people say geek culture is full of assholes.
As many have said, it's not fundamentally a geek problem, but a human problem. It's just that geek culture might reinforce those harmful aspects of humanity more strongly than other subcultures: at least in sports you do get to see the other teams' supporters and you do get to see your team lose. On the internet however, it's much too easy to just shut that stuff out.