You are supposed to root for Walt by default, because he's the protagonist. But he's transformed into a really nasty specimen, a man at least as morally bankrupt as Gus. Gus dressed nicely, spoke well, and had a code of honor--up to a point. He was still clearly a murderer many times over, and a pusher of dangerous and deadly drugs. Walt wanted (and got) that for himself. Being "out of the business" doesn't absolve him of anything.
I don't know that I've ever truly "rooted for" Walt myself, even at the beginning. There were times that you kinda felt for him a little, but he's always been a pretty selfish, petty, and egocentric guy.
Although even now, as far as he's descended, I don't think he's nearly as dark as Gus was. You can see that it still
pains Walt to some degree to have to hurt people or orchestrate their deaths (as he often spends long hours in a numbed state afterwards in his backyard), where Gus could slit people's throat without hesitation and without flinching.
Walt, as we see when he gets his ass kicked by Hank, still has to stuggle a bit to be a scary badass. He's still more of a weasel at heart than someone purely dark and evil like Gus.