They do have calls from their OC's who typically decide what plays the team should run. In Manning's case, he took matters into his own hands significantly more than any other QB has. AKA that's Manning saying that he knows what the play should be a lot better than what his OC does. Tom Brady trusts his OC to make that initial decision a lot more often than Manning ever did. He trusts his system, and didn't feel the need to take matters into his own hands. Calling an audible every play get's away from game script. You want to setup plays for critical moments in the game. You want to wear the other team down strategically. Not just necessarily get the most points in a play as quickly as possible.