The ones that make people cringe: the cloppers (which I actually have nothing against - I'd just rather that material was kept behind age walls), the ones who shove it down throats (I don't mean using a pony avatar but shoehorning it into threads/conversations), the ones who take it too seriously and rage (or worse, send death threats) over silly things, the ones who somehow manage to be misogynistic about it (how they manage this when it's a show about girl ponies in a matriarchy created by a feminist I have no idea), the ones who never shower (though this goes for a lot of geeks) etc etc. Are unfortunately quite loud. Also, just like the newspapers sell much better when they're all bad news, so does bad/ugly/cringey news about Bronies get all the clicks on the internet. It's just a human nature thing.
I use a pony avatar most places but only mention it on unrelated forums only if it's somehow actually relevant for that exact reason (both because I don't really enjoy getting torrents of abuse, and because wittering on about it in unrelated places is one of the things that bothers people )
The other issue was more in 2012 when it was a HUGE bandwagon - we kind of took over places like deviantArt (when I visited dA a few times back then, it was hard to find an image that was NOT about ponies, so I can see why people were frustrated). We didn't mean to, it was just a side effect of its popularity. But still, people did and still do hold us responsible for that.