Hate would be quite a strong word, but I don't really see the big deal of / dislike the following:
Background ponies: I don't mind them, but I don't really see the appeal
Treating fanon portrayals of characters as canon
If Fluttershy ever does something wrong, all is forgiven; if another character does the same thing, they're awful. Don't get me wrong: I love her, but I really dislike how they ignore her faults and treat her as something so pure and innocent. She has flaws and it adds layers to her character.
The Flash Sentry hate: I agree that he needs some character, but I dislike the fact that he seems to be disliked because Twilight shows interest in him.
Over-analysis of the show/ characters. It's not really my thing, unless it's a mystery series.
The attitude that you're not a true fan if you like/ dislike a certain season/ episode/ writer/ character, etc. We are all different and one man's meat is another man's poison.
How Trixie and Princess Luna are treated as the best characters ever. I like them, but it tends to get annoying when they are harped as, "best pony ever".