There's no problem if it's a minority. Then it's just a minor annoyance and kind of "stop liking what I don't like." As a majority, though? Yeah, I don't go to Anime Expo to see Homestuck. And yes, seeing them is an effect.
Let me put it this way. You don't mind Twilight fans, for lack of a better comparison. Sure, they tend to be kind of annoying, but you don't hate them because you're not a 3cool5u hipster kid. Then you go to a, I dunno, high fantasy convention, that aside from being fantasy (but the wrong type of fantasy!) has nothing to do with Twilight. Except, whoops, most of the people there are Twilight people and are doing absolutely nothing aside from having meetups which could just as easily be held somewhere else and adding to the gross and sweaty con experience. They proceed to do this at every con you go to, and most of the ones you don't. Their very presence is starting to bother a lot of the other congoers. Should they be allowed to stay?