Cena has been banged up for a while now and five weeks out of the ring will help him recover through minor injuries. Cena rarely takes time off and usually competes while hurt. The surgery allows his body to rest, which is important with the Survivor Series and the Royal Rumble coming up.
No matter how you feel about John Cena's gimmick, the guy is an absolute work horse and you've got to respect him for that. The amount of media he does for WWE + Make-A-Wish, etc is unbelievable and he's very over with kids. Of course, WWE depends on those kids in the years to come to keep WWE as popular as it is.