For instance, look at The Rock's heel persona back in 2003. The Rock's Hollywood gimmick was The Rock's greatest work as a heel. His Hollywood, snobby persona made for a perfect heel character. Although he was getting booed by most of the fans, there were some fans who still cheered for The Rock because, well, hes The Rock. They didn't want to boo The Rock no matter what.
Another example is Stone Cold's heel turn back in 2001. Stone Cold turns heel, joining forces with Vince Mcmahon. Stone Cold was at his best as a heel, putting on great matches with The Rock, Kurt Angle, Chris Benoit, etc. The fans hated Austin for turning his back on the WWE when he joined the Alliance but there were some fans that just didn't want to boo Stone Cold because they saw him as cool and edgy, especially since he saved the WWE from folding. Of course you were going to have a few who weren't going to boo him. Still doesn't mean he wasn't over as a heel.
One more example would be Hulk Hogan's heel turn and forming the NWO. Hulk Hogan turned on WCW by joining forces with Hall and Nash which shocked many fans. The fans felt betrayed at Hogan as well as the other WCW wrestlers that joined the NWO. Although you had many fans who felt betrayed by Hogan turning his back on the fans, you had people who loved the new Hollywood Hulk Hogan because they finally saw him as cool and edgy even though he was the most hated heel in wrestling at the time.
So it's not a case of CM Punk not getting over as a heel because hes already over as a heel. It's a case of some fans not wanting to boo him because of his heel persona which is seen as cool and edgy to them.