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.
Unless they did, in which case, my point is moot.
Edit: Of course, drawing from another source, you do have a point when it comes to Zuko from the Avatar series. He was a "villain" (that later became a protagonist) who was given even more of a backstory than the main character, and it was very clear that the audience was supposed to be sympathetic towards him, despite the fact that his single goal in life was to kill the Avatar.
Now I say this not to just engage in trivial nitpicking, but because I think his thesis needs to be refined. The author attributes his idea to a moral compulsion for people to support the 'good' company, or the one thats trying to slay a monster. What he's actually identified is the natural tendency for people to define themselves in opposition to the other. You can't be insanely loyal to a product unless there is a challenge to it. Its less good versus evil, its group loyalty vs. the outsider.