After the SuperBowl game, they signed him for the extension.
Based on things I have heard and seen I think this is what happened.
Money guys: lets lock him since QB prices will just keep going up, he is young and got us to the superbowl, so if we overpay now we will save money down the road.
Coach: he got us to the superbowl, is a good kid, and will keep growing, I think we can win with this guy.
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Coach: he is not growing, there is no development. (Almost every coach I know has a similar mantra of "get better every day", stagnation is the worst thing for a coach)- thus coach says, we cannot win with him.
Money guys: crap, oh well that gamble failed. again
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Money guys : guess we cannot trust our coach so we should stop gambling (my hope at least)