The point being is that, while Fanime may be an anime/manga-themed convention, the motto has always been By Fans For Fans. If the fans are into other stuff besides anime and manga and want to show their love for those things at the same convention, who really has the right to say otherwise? All it comes down to is some fans indulging in nerdrage and drawing lines that really shouldn't be there, since all they do is divide fans against each other.
This. So much this.
Been going to Fanime for five years now and its never felt like an "Anime only" thing. Sure, its the majority, but the most memorable cosplays I've seen have been non-anime. Last year there were a couple ginormous Transformers costumes that completely rocked and the Mushroom Kingdom SWAT Team kicked all kinds of ass. It's a convention whose underpinnings are definitely more "Fan" than "Anime", but even still, anime cosplay and culture still dominates.
To that end, the Homestuck hatred doesn't seem to be a matter of fandom, but a matter of quantity. The fandom is super popular, so it has a lot more people which means it contains, by rule of numbers, more difficult fans as well. Not to mention that the sheer number of the fans can sometimes create a "Mob mentality", which is where I think most of the Homestuck distaste comes from.
It really is the flavor of the month, though. Once Homestuck starts to lose popularity or end it will fall into place with the other fandoms and people will forget about all this. It happened to the Naruto fans, it happened to the Bronies, and now its happening to you.
You have my sympathies, but rest assured, the discrimination will weather with time. I wouldn't be surprised if the Homestucks got much more respect next year.
