To be honest, it's not the fact Jamie threw a boy about his son's age through a window, but the fact that he actually is in love with his sister what bothers me the most about the character.
*ETA: The fact that his sister is Cercei only adds a new level of messed-up to the whole thing as I see it.
I can't blame him for being in love with Cersei--he can't see into her head, so he doesn't know what a creep she really is. He thinks she's the other half of himself.
Given that they are Lannisters, I really don't blame them for the twincest. Who else is worthy of either of them, in terms of high birth, good looks, and wealth? Who else would understand either of them--what it's like to have Tywin for a father or Tyrion for a brother, to have lost their mother when they were old enough to remember her and young enough to need her? A Targaryen, perhaps, but they're all gone.
Who but each other can they trust? I really can't hold that part against either one of them. They probably feel as if they are a completely different species of human from the others they meet, in the first place. They were raised that way.
I do hold the attempted murder of Bran against him, but I remind myself that even Ned Stark might have done the same, if the alternative was to allow people to scald, flay, draw, and quarter all of the Stark children.
I agree that if Cersei hadn't been freaking out, and Jaime had taken a little more time to consider it, he probably wouldn't have pushed Bran--I think that was his soldier's reflexes at work. Then again, maybe he did consider all the possible scenarios, dismissed the ones in which Bran didn't talk as just too far-fetched, and pushed him after all.