My understanding is that Power Rankings weigh heavily how a team is playing now.
So, for example, even though the Patriots have lost a few games, they played really well this past week so they will probably move up. The Niners, even though they have won more games, didn't look good against the Ravens so they will probably move down.
Since the Niners kept the game close until the fourth quarter, they were playing on the road against a good team, and they had a short week, they may not drop 3-4 slots like some are suggesting, but......nine sacks doesn't help their cause. I think that one stat will have an overall affect on their ranking this week.
No worries....they are a young team and will improve.