The Jets have no one at QB, but last year they had less than no one (Geno Smith) and they did well in both games against the Pats.  Most of the Jets contests with the Patriots over the last five seasons have been decided by less than a score, and the Jets are better at QB than they were any of those games.

Patriots have beaten... Jags (1 win), Steeelers (4), Cowboys (2), Colts (3), and Bills (3).  Thirteen wins altogether.  And lets keep in mind, they didn't face the Cowboys team that actually won games, they faced the Bryantless, Romoless Cowboys.  The Jets opponents have a combined total of 12 wins.  So I don't see how you can consider that a relevant factor.  The only team New England played that you could argue meant anything was the Steelers with Rothlesberger, but we don't really know how good that team was.  Arguing strength of opponent here is pretty pointless.  Arguing the strength of defense is evenly pointless as the best defense the Pats have played are the 12th ranked Cowboys.  

Overall, the Jets have the 8th best offense in the NFL in terms of yards, and 7th best in scoring.  Obviously when you have the rushing attack they do, you're going to rely less on the pass (especially in goal line situations).  Just like when you have Tom Brady, you're going to be less reliant on your run game which is why the Pats rank 21st in the league rushing.   Plus, in the Jets victories they've been ahead by significant margins.  When you're up by two scores, you're not going to throw the ball... unless you're the Pats of course.  As for Fitzpatrick losing the game for them, he has only had two really bad performances this and last season.  Aside from the Eagles, he's been perfectly solid.

I'm certainly not going to argue that the Jets have the better QB, but contrary to popular belief, there are actually 53 men on a roster, not just one.  The Jets have the better offensive line.  Fitzpatrick has been sacked twice in five games which is pretty astounding.  Their O-line is outstanding in both pass protection and running.  The Jets have the better D-Line, especially now with Sheldon Richardson back.  The Jets have a better secondary.  The Jets have a better running back and a better running game.

The Pats have a significant edge in their receiving corp (Jets have better 1 and 2 receivers, but no other good receivers or tight ends) and their QB.  The Jets are better IMO at every other position.  QB obviously means alot, so the Pats, especially at home, will be the favorites, but the gap between these teams is really not that big.