You know King, I think that you and I may have been separated at birth. This is a great question, and it's something that I've always wondered myself. I've never really understood why heels are so popular in comparison to faces.
I think that it really took root once Stone Cold Steve Austin and The Rock emerged on the scene and really became the superstar anti-heroes. The attitude has shifted back to traditional good guy/bad guy roles since then, but I agree that there is a percentage of people who still really prefer the Austin/Rock way of doing things.
Personally, I like to cheer for the faces over the heels in general. There are some obvious exceptions to that, I'll never, EVER cheer for Batista and Chris Jericho will always be one of my favorites, but on the whole, I like faces better than heels in general. I thought that MVP is a better face than a heel and the same goes with John Morrison. Morrison in particular is much better. I always thought that as a heel he would go way over the top with his promos and he wasn't believable, but his mic skills have either really improved recently or he's really been shown in a different light.
As for John Cena, he's WAY better as a face than as a heel. People always complain on the internet that they want him to return to his old rapper gimmick, but that wouldn't make any sense. His heel character was designed and used as a way to get him some attention and to build up a solid fan base and it worked. He's insanely popular now, despite the very vocal internet minority.
I can understand on-line fans getting frustrated with certain wrestlers who are naturally predisposed to either a face or heel character and them getting booked the wrong way. For example, I've always thought that Triple H was a really natural heel (while Shawn Michaels is a natural face).
There are some wrestlers though who, even as faces, still garner a ton of respect from the internet community. The Undertaker is obviously the most prominent name. The same goes with Shawn Michaels and a few other big names.
Overall though, I think that one of the main reasons is that for whatever reason, it's "cool" to hate on faces and cheer for the bad guys. I don't really know why, but that seems to be the attitude.