I think he mostly was in his earlier years as a main eventer. But even then and before then, he has a few good/great matches. I remember it was said that Vince was impressed by the match Cena had with Kurt Angle at No Mercy 2003. I know he was in there with a wrestling machine but still. His matches with Brock and Undertaker in 2003 also weren't bad either.
I think around 2007 and so on he started to pick up as a performer. I'd never put him anywhere near the top of the list, but I've said it before and it needs saying again - you don't have as many good/great matches unless you're at least a pretty good performer. Batista was never the greatest in-ring performer either, but he and Cena had good matches with each other a few times, most notably at Summerslam 2008 and Wrestlemania 26, both which were normal, standard non-gimmick matches (ironically, their two hardcore matches at Extreme Rules and Over The Limit were my least favorite of them.) He's also had enjoyable matches with Triple H, Shawn Michaels, Umaga, Randy Orton, CM Punk, etc.
He's had a few sucky ones, too. His match with The Rock was even more average than expected. Thankfully, most didn't care about match quality when it came to that one. I never watched his iron man match with Orton but I hear it was boring, and it's obvious WWE made it a No DQ iron match because they knew it would be boring otherwise (to be fair, few people can wrestle for an entire hour and still keep interest throughout. There's only so much you can do in a whole hour without getting repetitive. One big reason I can respect Flair's work ethic for being able to wrestle so many one hour draws in his day, but it doesn't necessarily make me eager to seek them out and watch them.)
Overall, it looks like he fairs a lot better when he's in the ring with someone who's already an excellent performer but you can't argue he doesn't hold his own. It's obvious by watching more than a couple of his matches that he contributes and isn't just carried like dead weight throughout. You don't need an extensive move set to have a great match. It all has to with the booking and pacing and psychology of the match. Hogan/Warrior at WM6 is a good example. By all means, it should have been boring, but Pat Patterson's wonderful booking of the match made it a great clash.