The San Francisco 49ers were thoroughly destroyed by the Denver Broncos, and Peyton Manning had little trouble picking apart the 49ers secondary. He needed three touchdowns to set the career passing touchdown mark, and he had it wrapped up in the second quarter. He added a fourth in the third quarter as the Broncos rolled.
The 49ers went into the game with numerous absences on the defensive side of the ball. New injuries included Patrick Willis (toe), Chris Culliver (shoulder/hamstring) and Jimmie Ward (quadricep). The absence of Culliver and Ward resulted in some shifting in the secondary. Tramaine Brock returned to the starting lineup opposite Perrish Cox. When the 49ers went into their nickel package, Cox moved inside to the slot, similar to what Carlos Rogers did in the past, and Dontae Johnson moved to the outside role.
The new bodies apparently resulted in a simplification of defensive coverages. ESPN's Louis Riddick had this to say:
Given all the changes among the cornerbacks, and even among the inside linebackers (for coverage purposes), this is not remotely surprising. Tramaine Brock clearly was still rusty, with Jim Harbaugh saying after the game that had Chris Culliver and Jimmie Ward been healthy, Brock would have been much more limited. Dontae Johnson got what was essentially his first "start", and he got one heck of a lesson. It makes all the sense in the world that the 49ers would be in a much more limited scheme.
If you combine simplified coverage and a struggling pass rush, is it remotely surprising that Peyton Manning had a monster game? The 49ers will get back Aldon Smith, and hopefully see a return to form from Tramaine Brock. None of this guarantees they wouldn't get shredded by Manning in a potential Super Bowl rematch, but I think it is reasonable to at least be optimistic that things would turn out a little bit better.