Also, I think the reason people were rooting for Stringer is because I think most people saw that Stringer was smarter of a business man and at times more humble and caring than Avon. Then you see that Stringer is basically Avon's bitch when he's not in prison. When Avon gets locked up, you see a different side of Stringer because now this time he's in charge and running the show without having to run stuff by Avon (he still does run it by Avon in jail for posturing). You see he starts focusing on more legitimate businesses, and is really only doing the drug thing to keep Avon happy.
He's still loyal to Avon, even though he disagrees with a lot of Avon's ideals. You see how much he cares about Avon even though he sees Avon's self-destructive behavior. Not saying he's some selfless saint, but he was much more levelheaded to where people could relate.