Guess I'll just copy/paste what I wrote in a similar thread:

I can see why people would hate her, she killed some characters favored by some fans, tho I see it more as a byproduct of Eren's decision - her fault, but ultimately I think it was done to enforce the inner conflict within Eren, and to prove some points established by Levi.

Annie killed those people because they got in the way. Nothing more, nothing less. Asides from Petra, I can't remember the names of any of the former Levi squad, and my major feelings of sadness were directed mostly towards Eren. I would feel completely different if she went on another rampage and killed current squad.

The only example I can think of Annie toying with a life is when she took the line from a soldier she was holding ("let me go!"), and decided to screw with him. I think that was the only time I felt some sort of horror and disgust.

It's really easy to remember just the bad shit that happened and ignore all the good and tragic things about Annie. Her caring about her comrades, showing genuine happiness when teaching Eren how to fight, emotionally investing herself in the deaths she indirectly caused, looking horrified while apologizing to bodies, how her father was pushing her beyond her physical limits, being trained to fulfill her mission from early childhood, Armins speech to her about morality, the fact she screwed herself up the moment she couldn't bring herself to kill her comrades despite what the mission is - all of those things seem to be ignored by the large, and I can't fathom why. Annie is seriously more human then some other characters. Even my almost 60-year old auntie who watched the anime expressed her sympathy for Annie and pretty much nailed it on the head as to why she has been behaving like that.

Then again, it's obviously much easier to express hate and refuse to understand, or even try to comprehend characters and what their motives are. I mean just look at the horrible hate Historia got last month (and much of it was completely unjustified and blown out of proportion), and oh look, suddenly everybody likes her in this chapter! Yay! Yeah, I'm willing to bet when Annie does something awesome, and "good", suddenly everybody will love her.