The nature of football is that individual stats (at least offensively, defensively if you get a sack you get a sack) rely on the team having a basic level of competence so that, for example, the ball is snapped properly to the QB every single time before making a play so he can either throw it, hand it to the RB, or do an option play. The QB then had to throw the ball competently or hand it off competently as well, and then the yardage gets shared by the QB and the receiver or the RB.
As far as athleticism Football is a different beast entirely from other sports (man-to-man contact is legal and either expected or accounted for every play). Jordan could run circles around just about every other athlete in physicality (run speed, jump height, agility), but then Brady is also expected to tank takedowns from 250+ lb guys. Gretzky would likely come in second on physicality, and then it depends what age we're comparing Ruth and Brady, as Ruth relied on slugging a lot more than speed.
As far as Brady being "on Jordan level" the analogy is in the context of the sport he plays, not "is Brady a better absolute athlete than Jordan."