Actually, Tom Brady was treated differently because he’s Tom Brady. :-D
The NFLPA went to the mat for Brady because he and Peyton Manning run the NFLPA. The lawyers wrote the collective bargaining agreement, but Manning and Brady (and to a lesser extent Drew Brees) told them what to put in it.
For example Manning made sure of the insertion of a clause that either forced the Colts to pay him millions or make him a free agent without knowing whether he would be cleared to play after his neck injury.