It is a bit much to call Henry a brat–in fact, it is a bit unfair. Yes Henry hates Regina, but not without reason. 🙂
Regina obviously keeps him on a tight leash. And while I gave a small defense for her, her attitude in many episodes towards him can be seen as almost cold and the few glares she gave him when he defied her showed a spark of the Evil Queen. I don’t think she would ever hurt him intentionally (for now at least) but her actions have hurt him emotionally.
There is also the fact that she tried several times to kill his grandparents, and then took their happiness away and basked in their misery. Seperate Regina’s motivation (and despite the sympathy, I do not agree with Regina) for what she did for a moment and focus on the act itself, and how Henry views it. He sees his grandparents, he grew close with Mary Margaret, and all he wants if for them to wake up and have their happiness back. He cares for others like Jiminy and Ruby, and he saw how close Mary Margaret was to leaving Storybrooke and possible being killed. And he sees the hatred she has for Emma, and how she has gone to extremes to drive Emma away–that obession shows, even if Regina tries to hide it. He knows she killed off Graham (he felt guilt for that himself) and he seems to partly fear her wrath on others–he says it is good that Emma does not believe in the same episode, so that she won’t be next.