Well I think the rules were rewritten. It used to be the Brady/Manning rule, with a caveat that the rule was non applicable to all QBs on the Denver Bronco team. Of course now that Peyton is our QB, his name was removed from the first portion of the rule.
I kid, I kid, but I do seem to recall many discussions that the league protected Peyton and Tommy above all others. Not sure that's actually true. I think refs just mess up.