I don't think it's anything to worry about. Both of mine have liked the bad guys and the good guys at different times and pulled for each. I think it's probably because something appeals to them more about one character than the other, whether it's a good guy or a bad guy. Good guys aren't always written as likable characters. Remember Melanie Wilks? I don't know anybody that liked her, except maybe my mother. Everybody I know said she is too demure and a doormat and to be honest, even though she's a good guy, she's not anybody I would want to spend more than ten minutes with.
If you are concerned about it, ask him what it is about the bad guy he likes. Don't make a big deal about it, just ask and then say "oh". Ask about another character he likes, maybe a good guy this time. Do it a few times and see if you can figure out what he's picking up on and noticing. Kids can notice stuff that goes completely over our heads.
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I'm giving it another shot. We will see.
My forum is still there and everyone is welcome to come join as well. There is a private women only subforum there if anyone is interested. Also, there is no CAPTCHA.
The link to the forum is
http://www.rightplanet.proboards.com