The difference is one QB is expected to make up for the deficiencies of the entire team and when he doesn't he's considered a bad QB. The other QB has a solid supporting cast that can overcome his mistakes so he's (obviously) a better QB.
I see the same things out of Manning that I see out of JP, he has some great moments where you just shake your head in amazement, but he's also inconsistent throwing the ball and makes a few really bad decisions a game.