If there was anything working against Peyton it was all the hype around him... the same thing happened with Tebow last season. It seemed that the NFL or refs were afraid of looking biased towards Tebow last season and possibly Peyton this season.
Could you imagine if Peyton just waltzed his way to a championship after all the hype he got this season? Then the credibility of the NFL would be completely gone.
BUT... there is something HUGE to show that the NFL is not against Peyton... it's the way he is protected by the line. The refs let the Broncos Oline get away with murder all season protecting Peyton. Even in the playoff game he hardly got touched. Part of that is due to him dinking and dunking so much though.
Maybe what they let the line get away with in protecting him is why they are hard on him in other ways or not biased towards him there. They feel they are already gifting him enough.