I don't think that he was trying to say that people only root for genuinely good characters. He was saying that when we do root for the bad guy, we invariably

I don't think that he was trying to say that people only root for genuinely good characters. He was saying that when we do root for the bad guy, we invariably rationalize it to ourselves by finding ways to think of the bad guy as not being truly evil. "Misunderstood," or "noble savage," or "at least he has a personal code he follows faithfully," or at the very least, "not as bad as the other guys." We may start out subconsciously rooting for the bad guy because of our desire to see the plot advanced, but when we catch ourselves doing it we come up with some other reason why it's acceptable to root for the bad guy in that particular situation. We want to identify with the central character--if the central character is not a good person, we need to find traits worthy of our sympathy and/or empathy.