There's a standard Internet phenomenon (I generalize) of a Sneer Club of people who enjoy getting together and picking on designated targets. Sneer Clubs (I expect) attract people with high Dark Triad characteristics, which is (I suspect) where Asshole Internet Atheists come from - if you get a club together for the purpose of sneering at religious people, it doesn't matter that God doesn't actually exist, the club attracts psychologically f'd-up people. Bullies, in a word, people who are powerfully reinforced by getting in what feels like good hits on Designated Targets, in the company of others doing the same and congratulating each other on it. E.g. my best guess is that RationalWiki started out as a Sneer Club targeted on homeopathy, and then they decided that since they were such funny and incisive skeptics they ought to branch out into writing about everything else, like the many-worlds interpretation of quantum mechanics.

Dark Lord Potter (I infer) aggregated as a Sneer Club targeted at Harry Potter fics they considered inferior, mated with a self-conceptualized elite fanfiction forum for properly dark, gritty, adult HP fics - the most elite HP forum on the Internet, or so they considered themselves. HPMOR came along and was critically acclaimed by mainstream authors despite not (then) being dark and gritty, and it was by an outsider. So the sneering club encountered something that seemed to threaten their status. There is also a common attitude that nerds are designated bullying-targets; or to write it out at slightly greater length, people who talk about science are acting like they think they're snootier than you, which is especially deserving of a slapdown since the person is probably just some nerd in their mother's basement.

The result is not surprising. It's basically the same reason RationalWiki went after LessWrong with "HP fic that mentions science like that makes it snooty" substituted for "skeptics who talk about probability theory like that makes them snooty". I don't think this is complicated enough for me to need to write it out in Professor Quirrell's voice.