I would have agreed with you throughout the majority of the game, and then [SPOILERS] the ending sort of makes it understandable, since he's actually the villain. He's a selfish murderous psycho, and he's raising a girl in a way that might make her one, too. It kind of changes the tone of the game from "Sweet…

I also wonder if magnitude of violence helps separate it. I just finished The Last of Us, and one of the things that separates Joel from other survivors is the sheer number of people he kills. Yes, other survivors have had to kill, but no one kills quite like Joel. Characters even comment on it!