I've looked closely at this penalty issue. Most of the penalties called on us are those of our own doing. We have a total of 102 penalties called on us and of those, 47, or 46%, are pre-snap. Compare that to New England that has nearly as many penalties as we do (99), yet they only have 25 pre snap penalties, or 25% of their total. The average differential between pre snap and total is 34%, so we are committing 38% more pre snap penalties than the average of the other teams. We lead the league in false starts, offsides, and neutral zone infractions, and are tied with 6 other teams for the most illegal formation penalties. It's an important difference if you suspect that there is an officiating bias as pre snap penalties are very easy for officials to make and do not entail the same amount of subjectivity to them as do the pass interference, offensive and defensive holding, illegal blocks, and personal fouls. In addition, Pete's teams are notoriously one of if not the highest penalized teams in football. Pete himself acknowledged that his teams at USC were also very heavily penalized, so something else is at work besides the refs when it comes to penalties called on us.
Where the rub comes is in which team benefits the least from penalties called on their opponents. We are at the bottom of the heap BY FAR when it comes to beneficiary penalties. We've only had 51 penalties called on our opponents. The Jets are a distant 2nd with 63 beneficiary penalties. The league average is 80. That's some pretty solid evidence of a bias, but I'm still not prepared to cry foul as there could be some very reasonable explanations for that discrepancy, such as, it seems that predominantly running teams draw fewer flags being a run dominated team we should not expect our opponents to draw as many flags as a team that puts the ball in the air a lot. Us, the Jets, and Dallas are the top three rushing teams and we're 29th, 31st and 32nd in drawing flags.
Even so, if I was Pete, I, too, would be planting a seed in the ref's mind, regardless if I felt there was a bias or not simply because it's an argument backed up with some pretty compelling facts. Crying like a little baby sure worked for Jim Harbaugh last year when he started whining about our DB's the week prior to our contest in SF. I think we drew two holding penalties on the first series alone, so by no means am I trying to counter the arguments made in this thread that we're getting screwed or indicating that we shouldn't be crying foul.
Here's a link I think you guys might find useful. It slices and dices a bunch of stuff about penalties and goes back 5 years so you can see certain trends. Click at the headings at the top of the column and it will sort them so you can see how various teams stack up against each other in individual categories.
http://www.nflpenalties.com/