Personally, I disagree with this but it depends on how you define "Most Valuable Player". Are you voting for who you think was the best player or for the player you think was most valuable to their team's success? They're not always the same thing. If you pick the latter then the other contextual factors are already there. I don't think either way is inherently right or wrong. Whichever way you feel about it dictates how you would vote.
In this case, I think Rodgers was the best AND most valuable. He was off the charts good for 14 of 15 games and there was no doubt he was MVP. Brees gained ground because GB dropped a game to KC and Rodgers sat out a game + that whole yardage record thing. Rodgers threw 6 picks all season. Brees had a tremendous year but threw 3 in a loss to Tampa and 2 more in a loss to the Rams. Rodgers didn't throw 3 in any calendar month!
On top of that New Orleans had the better running game by a good margin (35 yards/game ranked 27th, NO was 6th). Green Bay's defense was ranked below New Orleans in points allowed (19th, NO 13th), total defense (last in the league, NO 24th), 3rd down percentage allowed (26th, NO 5th), pass defense (last, NO 30th), rush defense (14th, NO 12th). So I'm definitely not seeing where GB is better after subtracting the 2 quarterbacks.
Forgive this part, if it's been posted. I read a number of posts referring to this but didn't see exactly how the numbers work out (might've missed it). BTW, this part has nothing to do with my vote, but I was curious to see:
Brees actual stats: 468/657 - 5476 yds - 46 td - 14 int
Rodgers projected out to 657 attempts: 449/657 - 6077 yds - 59 td - 8 int