I think a lot of the negativity towards Cena is directly related to the time he came up through. Cena debuted post-Attitude era where most smarts hated anybody new who wasn't brought up through WCW, ECW or the territories because they "didn't pay their dues." That was also the time of the internet super-worker, so if you didn't have kewl movez, you were a bad worker. Smart fans are the easiest fans to work, so WWE started incorporating those elements into Cena's character. The 50/50 crowd reactions became the new millenium WWE Main Event style in the same way brawls through the crowd were a staple before that.
I do think that the WWE booking gets a little too cutesy for it's own good, because when they do try to book Cena into sympathy roles, he's pretty damn great. If WWE booked him a little simpler instead of trying to work the smarts, I think perception would be a lot different.