Someone/s in the Patriots organization (i.e., Belichick and/or Kraft) made a judgment and a decision after Brady excelled throughout the first eight weeks of the season and just before the Trade deadline:
The judgment was that, barring major injury, Tom Brady gave the Patriots a better chance of being competitive this season, next season and probably the season thereafter than Garoppolo or anyone else they could realistically add to the Roster in the immediate future.
The decision was that, since it would be impossible from any practical point of view to carry two Franchise-level QB salaries, they would try to get as much for Garoppolo as they could in a Trade and let the chips fall where they may by going with the guy who brought them to nine AFCCG's, seven SB appearances and five Rings. (Whether or not they didn't want to trade him in the Conference or decided not to condemn him to the Cleveland Dumpster Fire is purely a matter of speculation.)
Only time will tell whether that was the right judgment and decision, but, FWIW, it is the decision I would have made.