Makes sense when you consider the rules of it
|• It was based on an ethos of all positions created equal. This isn’t about the most valuable players; otherwise there would be a lot more quarterbacks. This is about looking at what is expected from a position and who most exceeded that.|
You expect the the most from the QB position, so, by the vary nature of this list, QB's are at a disadvantage.
So, while Newton was clearly above and beyond as a rusher, his passing wasn't exactly stellar. 60% completions, 17 INT, 5 fumbles...he was nowhere near the level Rodgers, Brees, etc. Brees still had 30% more yards, Rodgers still had 30% more TD's (that combines both rushing and passing for both), and Cam was less than average (18th) in accuracy. Was Cam the only the 95th best player in the league...no, definitely higher. But, their metric basically measures who out-performed the most last year. And in a year where QB's crushed passing records, his rushing wasn't enough to make up for it.
Now, get him to the 2nd tier of QB's in passing (63-64%, 43-4500yds, 25TD, 10-12INT), and the same rushing numbers, and you're looking at an MVP level year, and he's probably top 10 on that list.