Really? Or maybe we were playing to, I don't know, win?
There was 8 minutes and 48 seconds left on the clock on this play. By running the ball, the field goal was kicked with 8:04 left to play, and thus put the Bills up by a 3 score margin instead of a 2 score margin with 8 minutes left.
It is not necessarily the case that they didn't have faith in JP or they are keeping him on a short leash. Actually, I think it is the case that the Bills are very confident in their defense's ability to stop the Jets' offense at that point.
You run the ball, take 30 seconds off the clock to aid the defense, and then go up by 3 scores. Then you give the ball to the Jets offense, who hasn't beaten you at all in the 2nd half, and dare them to win the game.
If this team had an offense that was much more prolific than its defense, in the same situation, then you throw the football. However, you said it yourself - we are 30th in passing. Aiding the better of the two units, the defense, to win it at that point is a smart decision, not a stupid one.