From a 49er fan's perspective:
San Francisco's passing game stalled in the first half, in large part, because Seattle's physical corners were getting away with a lot of holding and PI, and at one point Alex Smith threw incomplete when a D-Lineman grabbed his face mask. Alex Smith also missed Kyle Williams a couple of times deep in the 1st quarter, but the number of times San Francisco's WR's were in a good position down the field prevented Seattle from jumping on the shorter routes.
At half-time, realizing the refs were not going to call many penalties on contact down the field, San Francisco made the necessary adjustments. The disadvantage of being overly physical on WR's routes is that the WR's have an easier time blocking, since they are in better position to do so. Usually when you see runs and check-downs going for decent yardage, it means that WR's are blocking CB's down-field.
Seattle's LB's are not terrible, but clearly are the weakest area of a very good, very physical defense. This gets hidden a lot of the time due to the speed and physicality of the D-Line and secondary, but when San Francisco was able to win on those levels, the LB's were exposed. They simply were not going to be able to stop the run without more help from the secondary and D-Line, while also trying to cover the short routes in the passing game.
