He was very much over. But a few months later the crowd started turning on him. Already in 2005, by Summerslam he was already getting boos during his feud with Jericho and then with Kurt Angle. When Edge won the WWE title in New Year's Revolution, the crowd was cheering enthusiastically, even though Edge was one of the most despised heels.
I think at the time people thought that he came to raw to lose that title to either christian or jericho. People wanted a few main eventers and for it all to appear like an even playing field. Instead, within two months after that massive pop, Cena had dominated Christian and was in the process of dominating Jericho. Fans were not ready for such a dominating champion yet.
Then WWE had him really go over Kurt Angle in ways that made Angle look weak and desperate. This was when fans truly turned on Cena and we finally got the schism that still exists today.
When Edge cashed in at New Year's Revolution...that crowd reaction was all ANYONE with intelligence would need to understand that Cena's time at the top needed to be curved to make way for new stars. Unfortunately, that didn't happen. I wish WreslteMania 22 would have been Edge vs Triple H. That would have been something to see. Hell, they could have made it a Triple Threat with Edge (c) vs Triple H vs John Cena. Maybe fans would have cheered Cena on then...and his victory would have been welcomed.
If it is one thing I have recently learned from Hiroshi Tanahashi and NJPW, it's that when you want people to constantly cheer your Ace babyface, you need to make that guy lose throughout the year so when you have him "overcome the odds" and win at your big event...people actually want to see it.
This isn't a lame John Cena bash, but that wasn't a Rock/Austin level pop, it wasn't on the level of Triple H's return, and it wasn;t on the level of Daniel Bryan late '13/early '14. Also, there were plenty of boos. Aside from that, still a nice pop.
Really over. He was the legit face of the WWE after he moved to raw. The booing really only happened around WM season with Triple H and HBK as his opponents and usually the raw after WM. The booing started becoming more noticeable after ONS when he faced RVD. I think thats when it became cool to boo Cena and I started to notice it happening more frequently at PPV's (He almost never got booed on Raw but PPV's were a different story)
He was really over with the Smackdown crowd but then he came to RAW and his character changed. It was really awkward. I remembered watching in 05/06 and I wasnt a smark at the time. It didn't seem right at all.