Because Punk's mug isn't "marketable" (they're right in a way, he doesn't fit the image of the company in 2013, maybe ten years ago though...), Cena still sells more merch (though Punk is number two), and Cena does Make A Wish crap, so of course he's the top dog. He's the face of the company. The problem is, they refuse to let anyone else be the face, despite the fact that WWE/F historically always had multiple faces that represented them at one time. When Austin was top dog, you had Rock sharing the limelight and for a point in time, Mankind. When Hogan was big, we also had Macho Man. When Bret was the face, we had HBK as his arch enemy.
Since Rock is gone, and Cena has the title again, and The Undertaker is gone for his year lapse time, I'm hoping we will have Punk/Cena feud again. The two have unbridled legendary chemistry in my opinion, they just need to let them work it.
The big problem is that I think Punk may have injured himself tonight. Hope he's okay!