CM Punk stopped being the underdog when he beat Cena at MITB 2011. At least in my eyes. If he didn't stop being an underdog then, he sure as hell stopped when he wrestled the Rock at Royal Rumble 2013.
I think what most CM Punk fans want is for him to get the John Cena treatment. Main events, make-a-wish, TV shows, Talk shows, Radio shows, parades, merchandise, and the ultimate "this guy is the face of the WWE" title. Personally, I'm perfectly fine with where CM Punk is now. Do I wish he was in the main event of Wrestlemania 29? Definitely, but it doesn't really make me think the WWE is holding him down. How could they? He's the longest reigning champion in the last 25 years! What else could you want, like you said.