I seconded Emiya Shirou from Fate Franchise. Many girls and boys dislike him since he is a "straight" character, but I believe he does not deserve that much hate.

The second one would be Near from Death Note franchise. Probably because there are soo many L fans out there, think that no one could replace him. I don't understand why so many fans dislike Near. He is a decent character, but not bad at all.