I think, in a way, it doesn't really so much matter when the Cena hatred started. I say this mainly because it's here, been here for some time, and doesn't stand much chance of going away.
Personally, I like Cena. Don't really care if that offends people. At the same time, though, I will agree that he could use some freshening at this point. I personally think he should go back to the old rapper gimmick, but since that was really a heel gimmick (and there's no way they're turning him heel with his merch sales), and they've gone PG, I don't see that happening. I admit I hate his entrance music. I sometimes think that the sound of his music is what gets people angered more than actually seeing him.
I think the problem with Cena right now is the same thing that gets the crowd to turn on Triple H at various times: he's almost always feuding for the belt or has the belt. Personally, I blame this on the creative/booking decisions. Used to be, way back when, that they could build feuds around guys for reasons other than the belts. Yea, the "this is personal" crap is overused, but sometimes that's really all it takes. If they actually moved these guys off belt feuds once in a while, I think it would help prevent people from getting tired of seeing them. I kind of expect this to happen to Orton eventually, too. I'm not sure why people haven't turned on Batista yet. Cena has had more good matches than Batista, not that that's saying much at all, but he can also talk better than Batista and yet Batista is universally loved, it seems. Hopefully they turn Batista heel because he could use it.
A bit off-topic here, talking about the creative decisions. One of the problems is that they seem to start silly feuds. Right now they're going to have MVP feud with Regal. I like both of those guys, and I know it hasn't been done before, but after you have MVP wrestle Orton and then Rhodes, having him feud with Regal will do nothing to give him any momentum on Raw. This isn't a knock on Regal, but his status is always mid-card, and not even upper mid-card. So creative isn't really helping MVP right now. The same goes for Cena now feuding with Big Show. Obviously they need to wrap up the ridiculous stunt from Backlash, but these two have seen each other enough. Let's move them elsewhere after the feud. Maybe finally have Cena feud with Miz? Could only help Miz in the long run. Maybe Matt Hardy, someone, anyone Cena hasn't feuded with in his time. This also applies to John Morrison feuding with Shelton Benjamin on SmackDown. Should produce some great matches, but can't see either guy gaining a lot of momentum from a feud.
So, yea, the Cena hatred is palpable, and in my opinion, largely ridiculous. I think most people who boo Cena do it just because it's so "trendy" or "cool" to do it. If it's true that the internet wrestling community only makes up about 10% of the overall fan base, it just goes to show that a lot of people can be easily swayed by a precious few. But, like I said, it's getting to the point where I can see people booing Cena for legit reasons, not just because. That being said, I don't see anything about Cena's character changing anytime soon, so we're stuck with what we have.