Confidentially/gag clause if he wanted to show them up he would have gone to court. It will be settlement without admission of any liability/wrong doing by league. Its a piss off payment and he took the money and ran. Long term message to NFL players if you want to get on in the league tow the party line. America is the land of free speach as long as you stick with convention.
If he was right or wrong he ended his own carear by leaving 49ers no other team was going to take him on as he would cost teams money/support with his views. Being a wife beater/dog fight organiser or drug user is an easier come back than protesting the US flag, mad country.