He lost his #1 RB for several weeks. Lost his best WR for the season in week 4. Hollywood Brown was injured in preseason and didn't play the entire regular season. Went undefeated at home and only lost 1 road game in Buffalo (I am not counting the 38-0 loss in week 18 in Denver when they played the backups). They did all this despite every team gunning for the 2X defending super bowl champs, week in and week out.
I am not saying a case can't be made for Quinn, Campbell or O'Connell. Heck, you can make a case for either of the Harbaugh brothers.