The Pats have a better pass defense, the Broncos' run defense is far superior. You can pass on the Broncos. You can pass for big plays on the Broncos. The Pats haven't been giving up big passing plays this year.
In fact, I can think of two huge passing plays that the 49ers blew with wide open receivers who dropped the ball. There was a play where Vernon Davis was wide open up the seam without a receiver within five yards of him and he dropped a ball right into his bread basket. Another play had Boldin wide open on a crossing route right outside the end zone that he dropped which would have been an easy TD. The 49er offense had the opportunity early to exploit their defense big time, but shot themselves in the foot. Later in the game they forced Kaepernick to be a gun slinger and he sucks at that.