This was the scrimmage day. If it was a normal practice day, you might have a stronger argument. But this might be the last time that the 1s play in a game type of environment before the start of the regular season. At this point, there is nothing Cam could do to lose the starting role. All that could happen is Mac taking it from him and he cannot do that standing on the sideline when the 1s are on the field.
If Jones had a legitimate shot to start on September 12th, Belichick would give him every opportunity he can before the start of the regular season to play in real game conditions with the 1s. He didn't need a rest today with two more days before the game. Starting Cam today didn't reps as much as Jones if it was a real competition.
Besides, it isn't like Jones had less reps today than Newton. It was just that he did it with the 2s and 3s while Newton did it with the 1s. If it was a rest day for Jones, he wouldn't have taken the field at all or just did a few reps to keep him from tightening up.