Dat's cause of bronies who show themselves too much. When bronies were from 4chan subculture, no one did notice them. Here's da explanation, chestnoye slovo.
We're a very clique oriented species. If someone deviates ever so slightly from what society seems to have dictated is "the norm," all hell breaks loose. Look at nerd/gamer culture. Not so long ago nerd culture wasn't a thing. You were ostracized by society for gaming or watching cartoons/etc past a certain age. Now these things are in style or hip. It's OK to be into these things, society tells us. Pardon me if I am rambling, but I basically mean to convey that we are today's nerds.
Because the vocal minority makes the rational majority look bad. There are lots of people who push being a fan beyond the bounds of societal norms in different & distinct ways... which is to say, as one specific example, I do not care so much that someone may own a giant MLP plush but I am absolutely going to care if someone starts loudly & publicly describing their X-rated encounters with said giant MLP plush. That's what the public is interested in hearing & that is the type of story that sticks in their mind when they hear about bronies. The bronies who sit quietly & enjoy the show are not interesting to hear from, or interesting to hear about. Unfortunately with bronies there are multiple different distinct types of vocal minorities at work, so it's much more invasive & much more likely to find something that would offend the common nonbrony.