Cena has lost cleanly his fair share of times as well. He's lost to Batista, Triple H, Orton, The Rock and CM Punk (three times) without cheating or interference. He's lost to a few others when there was cheating involved but as mentioned, top stars the caliber of Cena don't lose that often. They're supposed to look mostly unbeatable to the vast majority of the roster the vast majority of the time. Hogan only lost cleanly once by pin fall and otherwise only lost three battle royals without cheating involved. Austin lost cleanly about 4-5 times, but still won 95% of the time. Cena isn't much different at all than his predecessors.
You could honestly make the argument that Cena loses more times than any other top guy has. A big reason for that is no doubt that he's been on top longer than anyone else since the modern day format of weekly build and star studded matches on Raw and Smackdown and monthly PPVs that was introduced in the 90's, but still.