I don't think it's so much the fandom's fault most of the time, honestly. Every fandom has its good and bad, but with the really popular ones (Hetalia, Homestuck, MLP, etc.) they simply have more people and thus a higher likelihood of encountering one of the bad apples.
It's been my experience that it's been kinda rare for me to run into someone that rubbed off on me the wrong way, but perhaps I'm just not a magnet for it or anything. I've run Fanime's Vocaloid gathering for two years and never really had an issue, and my only negative instance with the MLP fandom was the time at Fanime where I realized a guy I'd previously been talking to was following me around (but it wasn't difficult to escape and the situation didn't really get any worse.) But that was one brony out of the god knows how many I've met, and creeps will be creeps regardless of the fandom they're in. /shrugs
I dunno, I guess I just see fandom-shaming as being a bit unfair.
Winter SacAnime // Sakura Con // Equestria LA // FanimeCon // Everfree NW // BronyCon // Summer SacAnime // Sac Brony Expo
Ultimate Madoka, Puella Magi Madoka Magica - 93%
Fluttershy, My Little Pony - 85%
Cocoa, Fisheye Placebo - 100%
Gumi (Camellia), Vocaloid - 50%
Rainbow Dash, My Little Pony - 60%
Fionna, Adventure Time - 70%