Yeah. He has no such solid reason to hate Konoha as Sasuke does, for example. He was used by Konoha like any ninja was, but also given quite a lot of freedom. When he went beyond that freedom with his demented experiments, he was driven out. He joined Akatsuki, one of the worst rogue ninja organizations, which surely was a reason enough to put a bounty of his head. In the end it was all his own doing, so there's no reason to hate Konoha hidden there.

He's simply evil. Maybe not as evil as some since his main interest isn't being evil, but he's evil nonetheless.