I think Cena is looked down on by so many because he has so few guys who realistically could beat him. This is down to (a) poor booking for sure, i.e. the SuperCena thing, but also (b) not enough talent being booked properly. Cena became interesting over the summer because there was a guy who rose up and seemed to have been made, via booking or via chance, a legitimate threat to Cena - that man was CM Punk. When that happened, I was far more interested in Cena's feud than I'd ever been. Punk is getting the love right now but only because he rose up and became the first man to legitimately threaten Cena's reign. Unpredictability = ratings. Look at Punk now - questions now being raised over whether he is as good as we thought due to a lack of legitimate contenders with Cena out of the picture and hence the love for Jericho as a legitimate rival to Punk. That's been the problem with Cena for so long - he was forced down our throat (to an extent) a few years ago and he continually defeated the likes of Jericho, Batista and Orton until they no longer felt like a threat to him and therefore Cena's feuds became boring and predictable. When new guys did beat him, it was never clean (Sheamus for example, four way and tables) and meant that we kinda knew what was coming - Cena would win in the end, predictable, boring, Cena gets the hate.
Brings me to Rock. His reign in the WWE was far less predictable. If we compare Cena and Punk now to Rock and Austin back in the day - fair enough comparison as the two genuine biggest stars. However, Rock and Austin rarely held the title for a long time - Austin had one long run (WM17 > December 01 with Kurt holding the title for two weeks in the summer), Rock rarely had more than a couple of months. It was the other guys on the roster that made Austin and Rock the stars they are - you always felt like Rock and/or Austin could lose their titles, good booking. With McMahon on Austin's case and guys like Triple H, Kurt Angle, Mankind, Undertaker, Kane, HBK, Jericho and the late Benoit to name but a few, their feuds were always interesting because you felt like they could lose. How often do you watch a PPV and think it's 50/50 here with Cena in a one on one match? Apart from his matches with Punk last summer, when has it happened? It doesn't, it's predictable - if Cena loses, he loses in a cheap, unclean way and then he'll get revenge down the line, predictable and boring. Hence the reason Cena generates so much hate (escalated by his cheesy, goofy, kiddy friendly style as well).
The likes of Alberto Del Rio, Christian, Daniel Bryan, Sheamus, Dolph Ziggler, Wade Barrett and Miz are not a threat to Cena because they've not been built properly. Look at Miz' title run - he beat Orton with the MITB, beat him in a rematch at the Rumble in a dirty way, struggled to overcome Lawler and then did it in a Ladder match, needed Rock to beat Cena at WM27 and then lost to Cena at Extreme Rules. Where did Miz ever get the big win in that title run? Answer: he didn't. I can accept he is a heel and should get heel wins but he also needs big wins that cement him as a legitimate threat in his own right. He never got one. Heading into Extreme Rules, Cena was the clear winner because Miz was a weak champion. It happened again with ADR over the autumn of last year. It happened with Barrett when he led Nexus - he needed a big win over Cena in that white-hot run he had, it happened with Sheamus when he burst out, won the title but then Cena overcame him without taking a clean loss. The WWE books Cena and his opponents wrong, the fans turn on Cena. Which is why he'll never ever be as respected as Rock - wrongly because Cena is more committed and loyal to the WWE than Rock was/is (no slight on Rock but Cena's loyalty is unbelievable).
At WM28, I will cheer for Rock but I hope Cena can have a great match with him. I can sense a Cena heel turn at WM28 and it would breathe new life into his 'stale' character (stale with the adult audience, anyway). I hope people will learn to respect Cena in time and realise that the booking him and his opponents have received is what has made the product predictable - it's not Cena's fault.
So, to sum up, Rock > Cena - but it isn't Cena's fault!