I think people just don't like Eren because his superpower is...surprisingly useless. Most of the time is spent trying to figure out the titan ability and opportunities to just use it as a weapon are surprisingly little. The times that other titans attack his group, they're usually outnumbered or they're up against stronger titans than he can handle. And because of his power, he keeps getting kidnapped, so he's pretty often the damsel that has to be rescued.
AoT has a Brains, Brawn, Will sort of thing going on. Mikasa is the toughest one and the one who will continue the fight no matter what. Armin is the brains and is the one who most often acknowledges the moral uncertainty of their situations. But Eren is the Will. He hates the titans more than anyone else and is the one who wants to kill them. Mikasa will continue the fight so as to 'live', but she doesn't really have strong feelings on the titans and Armin is driven by his love of his friends more than anything. But Eren is driven by hatred. He will fight the titans not because he wants to live or because he's devoted to his friends, but just because they are his personal enemy.
Jesuotaku did a pretty good analysis of the show relating to that sometime ago, you should watch it if you're interested.
Edit:
http://blip.tv/jesuotaku/attack-on-titan-an-in-depth-analysis-6774120 here it is