The thing with the crowd and John Cena is that it simply isn't what it appears to be.
Like D-Man said and I've said in numerous posts regarding Cena's popularity, Cena's "unpopularity" with the "Let's go Cena/Cena Sucks" chants has become something of an unofficial tradition in WWE. People participate in it because it's fun. If the crowds didn't care about John Cena at all, he'd be getting the Tensai treatment and would have been a very, very long time ago.
I've been to a good deal of WWE house shows and I've seen 12 year old boys dressed up in John Cena gear participate in the "Cena Sucks" aspect of the chant while I've also seen 18-40 year old males, the demo that supposedly "hates" Cena, wearing his gear and saying "Let's Go Cena".
Whenever you turn on Raw or SD!, it's easy to see a lot of fans in the audience wearing Cena merchandise. If "everyone" really "hated" Cena as much as some think they do, Cena wouldn't be in the spot he's in nor would he be making money hand over fist for the WWE.
At the end of the day, it all comes down to money just like it's supposed to. And that is where the fans generally have an impact on who WWE pushes. The reasons why WWE continues to push guys like Cena, Punk, Bryan, Kane, Ziggler, Rock, Lesnar when he's around, Taker when he's around and many others is because they generate a positive response from WWE fans, whether they're being booed or cheered, and are helping to bring in a lot of money for the company.
From an overall perspective, Ric Flair was probably the overall best & top heel of the 1980s. He was the one that Jim Crockett, Jr. built his company around during the 80s despite the fact he was a heel and despite the fact that he got "booed". The reason Crockett did that is because Ric Flair made a lot of money. Flair was good at his job of course, but if you can't make money, then it doesn't really matter how good you are.
As far as Punk being heel goes, exactly why shouldn't he be heel? Just because it's what a handful of people want? Punk has easily been the top heel in wrestling during his heel turn. Punk gets a decent amount of cheers sometimes, depending upon what town Raw is in, but he constantly gets more boos than cheers now. From a character standpoint, I think Punk has been much stronger than he was during his babyface run at the first half of 2012. It wouldn't bother me if Punk became a face again, but I think they need to go back to more of the edgier, anti-corporate rebel he was back in 2011. Punk is a money maker for WWE so it doesn't really matter if he's face or heel. Fans still gobble up his merchandise like it's candy.
I get that some people want Cena to go heel. For me personally, I'd like to see it take place. However, I know WWE won't do it just for the simple sake of turning him heel, nor should they. It'd be a stupid business decision. Cena is popular with young fans who aren't quite as jaded or knowledgeable of wrestling and it's ins and outs, at least most of them aren't, and they make up a healthy percentage of Cena's merchandise sales. As long as Cena continues to pull strong audience interest and make lots of money for WWE, he won't be going heel. Also, you have to consider the possibility that make Cena doesn't want to go heel. If anyone in WWE has the stroke to determine whether they're face or heel, it's John Cena. Cena is also a damn good public relations guy for WWE, especially when it comes to WWE partnering with charitable organizations like the Make A Wish Foundation,