Funny one that.... It seems to me that the cheers and boos (he received both at points) were simply from different sections of the crowd.
When he and Kane were up the ladder right near the end, you could hear cheers as Kane got the upper hand and then there were both audible boos AND cheers when Punk eventually knocked him back down a rung or two to gain control of the situ... He still got a pretty damn good pop when he got the win too.
The biggset shitter about Punk's win is the fact we didn't get to see him cash in on a newly crowned Orton, finally gaining retirbution for Unforgiven 08 and kicking off a full blown fued between the pair of them.
As for what to do with him?
Yeah, a fued with Kane seems pretty likely and depending on the brand there's plenty of decent mid-card talent for him to fued with until he 'cashes in' (MVP, Kennedy, Christian, Umaga, Shelton, Jeff H, Kofi), but as our thoughts turn towards his title shot:
Face: Obviously none are holding titles right now, but Edge, Jericho & Orton all immediately spring to mind in terms of potentially good title shots/fueds... In fact irrespective of titles, these 3 would prob top my list of prospective punk fueds.
Heel: HHH.... Well after WM it's quite apparent this wouldn't do any good for Punk. An unsuccesful shot at Cena would be cool for character/stroryline development.