I also think that some fandoms are hated on because they are incredibly large. Homestuck, Hetalia, MLP, Naruto, Bleach, etc, are so incredibly massive (Naruto and Bleach not so much anymore, but you occasionally see people), that I think people get overwhelmed a little bit, and some get tired of seeing the same character over and over again. And you also hear stories of bad apples, and sometimes drama and elitism within said fandom. Shipping wars can also be scary. >.<
But one mega pet peeve I have is when people judge you based on the fandom your in. Don't judge people based on what they like. Get to know them as a person before you go making assumptions that they are like the few bad apples within the fandom.
Kairi- Kingdom Hearts I (50%; on hold for now)
Nepeta Leijon- Homestuck (5%)
Yuffie Kisaragi (Original Christmas Design)- Final Fantasy VII (Based off of AC, 5%)