Just because we don't like generalizing people doesn't mean we can't point out legitimate and endemic flaws in the Sonic fanbase. They're pretty clear and identifiable. There's two major problems.
For one, Sega in part brought this upon themselves by constantly trying to reinvent the main Sonic franchise with virtually every new installment, in contrast with Mario's many successful sub-franchises. As others here have said, this has brought upon a massive case of Broken Base factionalism, with so many fans clinging to an absolutist interpretation that every game must be like their favorite game. Since fans disagree heavily on which games or characters are the best, there's little hope of reconciliation, and that ties into the second problem.
The most unfortunate thing, and I hate to bring up generalizations, is the demographic makeup of the fandom, which leads to many of the negative actions typically associated with the fandom. It is largely made up of kids who are too young for the Internet, or adults who are nostalgia-obsessed and, to be painfully honest, have a mental disability or other issues going on in their lives and probably shouldn't be on the Internet unsupervised. They tend to be overly emotional, have poor social skills, and live through fictional characters as a result. This "vocal minority" isn't a minority in this fandom. It's legitimately hard to find a decent, respectable person in the Sonic fandom without running across these kinds of people these days. Their works are everywhere, and make themselves and everyone associated with them look like fools as a result.
Naturally, you find some of the same kind of people in the MLP fandom, and some of the perception issues dealt with here are the same, but there is a still a strong contingent of respectful and decent fans. Likewise, the Sonic fandom still has a number of respectful, creative, and talented people, but they unfortunately seem to be the minority. More kudos to them for sticking through it.
EDIT: Really good read.