Tom Brady does a lot of things outside of statistical valuation. His leadership and ability to read and decipher defensive packages is peerless. Only Peyton Manning was on the same level in that regard.
He also provides his team with a wealth of experience and is the hardest working guy in the organization nevermind the locker room. No one ever hated on Brady for not honing his craft or putting in work.
Then you look at the fact that his stats ARE good at this stage of his career, so he isnt even being defined by the intangables. He lead the league for a good part of the season in yards per attempt, and was the most accurate on those throws. Not only that but he isnt turning the ball over, something he should be doing at 39 years old.
Bradys value is actually discounted if anything. He is the best QB ever, and its not really an argument.