Just like The Rock, who fans don't care if he's a heel, didn't care if he was a heel when he went against Cena (which he clearly was) because they have such large crushes on them. These are the "I wish I could be like" guys, often misrepresented on the internet as "that's what I'm like!".
It's 'cool' to back the bad guy, just as it's 'cool' to root for the antagonist in a movie. Much of that is the case here. Of course it doesn't hurt that, like The Rock, Punk is so charismatic and good at what he does.
Wrestling hasn't really changed. The fans have.