The WSJ today had an excellent analysis of why Denver lost.
Essentially, it was the ability to pressure Manning without the blitz. They rushed either three or four all day. This allowed an extra linebacker, or even a lineman, to sit five yards out and wreck the pick, while at the same time preventing single coverage receivers from burning secondaries with yards after catch.
They tackled the ball carrier and not the ball as well. Something that seems to be lost on a lot of defenses that were relegated to sitting at home and watching the game on TV.