In response to Low-FB-IQ's comment:
Same problems, different year.
Anyone that thinks that game was close was watching through rose colored glasses. The 49ers kicked the Pats butts all over the field. The Pats did not beat themselves, the 49ers forced the mistakes with better play.
This is very true. The coaches film isn't available yet, but I just re-watched the condensed version of the game. On offense, I see too issues:
1. The O-line was not effective against the 49ers D line and LBs
2. We don't really have enough receivers who can stretch the field or get open downfield
In the second half, the 49ers really backed off on the rush, sending just three a lot. At that point, we were able to come back with short, quick passes. Lloyd also gave us some help on the outside and deep, but none of our other receivers was very effective outside the short part of the field. Even when Brady had time, no one was open downfield. The most effective plays were those where the 49ers sent four and Brady got the pass off fast to a short receiver. If the rush was too fast though, Brady got sacked or the pass was off or to an unready receiver.
Really, this scares me, because as Low FB-IQ says it's the same problems we've seen against other good defensive fronts--the Giants in 2011, the Jets in 2010, and the Ravens in 2009.