Honestly the refs aren't playing favorites, people only perceive it that way because of one or two high profile no calls or something. Here are the stats for amount of roughing calls per QB for the last 2 years.
Quarterback Calls per 100 passes
J. Campbell 1.46
J. Cutler 1.28
C. McCoy 1.20
J. Clausen 1.00
S. Bradford 1.00
K. Orton 0.99
M. Stafford 0.93
R. Fitzpatrick 0.91
M. Vick 0.88
D. McNabb 0.75
S. Hill 0.72
M. Cassel 0.72
C. Palmer 0.68
C. Henne 0.67
D. Anderson 0.61
J. Kitna 0.61
P. Rivers 0.60
M. Ryan 0.58
K. Collins 0.53
A. Rodgers 0.52
D. Brees 0.51
A. Smith 0.48
R. Grossman 0.40
M. Sanchez 0.32
B. Favre 0.28
B. Roethlisberger 0.20
M. Hasselbeck 0.18
J. Freeman 0.17
E. Manning 0.16
T. Brady 0.16
M. Schaub 0.15
P. Manning 0.15
D. Garrard 0.00
J. Flacco 0.00
K. Kolb 0.00
T. Romo 0.00
Other* 0.73
Obviously the refs favor the likes of Jason Campbell and Jay Cutler. lol Brady and Manning actually get the fewest calls (no doubt partially because they don't take a lot of hits, they are timing and rhythm based passers and don't scramble around too long) both only had 1 RTP penalty in the last 32 games, but it goes to show perception can be different than reality.
It's also amazing how I was pissed when someone got Chris Johnson before me in my money fantasy league but I was just looking at the stats and Chad Henne has more rushing yards than him. lol
On top of that LeSean McCoy, Fred Jackson and Ahmad Bradshaw are all dominating for me along with Brady, Megatron, Jeremy Maclin, Steve Smith, Aaron Hernandez, Vernon Davis. My team is looking unstoppable at the moment.