I feel that people hate mainstream anime (Naruto, One Piece, Fairy Tail) for one of 4 reasons,
1. They tend to be slow paced and focused on character develompent (Not everyone's cup of tea).
2. Because of the constant demand for material mainstream anime often use fillers, however I feel that in one piece, Fairy Tail and to a lesser extent Naruto, the filler episodes weren't done that badly, if you hadn't read the manga you probably wouldn't be aware that they were not part of the storyline. (Anyway if you don't like filler, skip it)
3. People hear too many good things and have such high expectations that they are dissapointed with the end product. (Try to legitimately compare a mainstream anime to some of the more obscure titles and they often fare pretty well)
4. People feel that if they like mainstream anime like they aren't unique, so they make themselves hate stuff everyone else likes so that they seem edgy... (I know a lot of people who are like this and incorrectly pronounce japanese titles to seem more advanced or whatever, even when those anime have english titles...)
Anyway... stuff I didn't enjoy...
Chobits - so very very boring having a main character with no personality or memory.
This Ugly Yet Beautiful World - Same problem.
Elfen Lied - Hmmm... I sense a pattern to my hatred, maybe I'm just not a fan of the whole Amnesia to stagger character background development... Plus it always just seems too convenient, like despite being tortured or a destructive force or whatever that polite and obedient is the opposing factor...
...I also think it's why I hated Tsubasa Chronicles compared to Card Captor Sakura, because in CCS, Sakura was awkward at first and developed into a bad ass, or at least developed enough to fight on her own, and in Tsubasa Chronicles she's just this useless princess incapable of doing anything...
So I guess that's hatred of a story mechanic than an anime in paticular...