I think it's a combination of:
- people feeling some of the things he says are pretty..... stupid. Guess that's what you get when you can't say '
****', 'jackass' etc.
- he represents the PG era of WWE (though people were booing him back during his first title reign in 2005, so that came later)
- him being in the main event scene for so long, when people don't see him as that good a wrestler (anyone who uses that criticism against Cena but are Rock fans are just trying to come up with things to bash Cena about IMO)
- and I think him coming along after Rock and Austin didn't help him either. Two of the all-time greats were always going to be a tough act to follow.
Personally, I don't mind him that much, I think a lot of his hate is unwarranted, but I can kind of understand where it comes from.