I'm bullshitting heavily here, but I'm guessing it's some combination of the "Nazi bar" and "vocal minority" ideas. "Nazi bar" (
a term I'm stealing from Tom Scott), I'll use here to mean a place that is so tolerant that it ends up tolerating the intolerant (or rather people you wouldn't ever tolerate), and driving the good people away from it because of it. Same way in which you won't go to a bar if you knew it let Nazis hang out in the basement. You wouldn't tell your friends, at the very least.
Fandoms tend to be very tolerant, often to the point of becoming a Nazi bar; you see this in spades in the furry fandom, where you have these, uh, "Nazi furs", which are exactly what you think they are. At least there, most furries upon seeing someone so pridefully propagate hate, are rightfully vehemently against these groups. The furries are mature enough as a fandom that they're able to drive out the Nazis (and each other, I think?). They do exist, of course, but they haven't overtaken the fandom.
In a younger (audience maturity-wise) fandom, though, they don't have that drive-out mechanism. That's how you can end up with total weirdos in a fandom. They come in, they're fans of the work in question, but they have this thing about them that's extremely unacceptable in modern society. Just, like, imagine the things that would instantly repulse you from a person if they were that. So you have these weirdos, and they're rising through the ranks of the fandom's society (insofar as a fandom is a society) over time, right? Wouldn't their weirdness, their extremely-unacceptable thing(s), eventually spread throughout the fandom as a whole?
And when the weirdos are in charge, that's where all sorts of shit can go down. King, you've mentioned the MLP fandom, that's a prime example. I think the thing that drives the normal people out (the people who don't have the extremely-unacceptable thing about them), apart from the Nazi bar effect, is a vocal minority. Even if they're only a minority numerically, weirdos tend to be really good at being vocal about their weirdness. The normal people in there bail out of there because they don't want to be associated with the weirdos that share a fandom with them.
So now you reach peak weirdoification of a fandom. The normal people who formerly occupied that space have ejected long ago, and in their place are like-minded weirdos, (fantasizing about) doing unspeakable things to the characters they
appear to idolize. At that point, all you hear about that fandom is just the escapades of those weirdos. You go on DeviantArt to look it up, you just see... things. Unholy things. There's still normal people in there, doing normal things, but if your first experience was
that, I think you're justified in writing off the whole fandom at that point.
Strangely enough, I think it's a reversible process. I heard that the Undertale fandom actually became normal again after a while, after it stopped being in the public eye. I'm speculating (as if this whole thing isn't speculation enough) that it's a demographic shift. All the young kids moved out because it wasn't "in" anymore, so the average fandom maturity shifted upwards over time. This let them drive out the weirdos in the fandom (because you don't get all these kids going "but we have to be friends!"), and I think it's mostly normal people now. So I've heard, anyway.