That isn't the way the league endorsement rules work. Just like socks, hats, shirts or anything else, the league gets a crap load of money from certain companies to endorse their products and players have been fined for years for wearing or using other companies products. Kaepernick can endorse Beats all he wants - just not right before and after the games. And he really should keep quiet because if it comes out that Beats paid his fine, that is blatant violation of the NFL CBA rules and he could get in trouble for that.
I believe the CBA does not allow teams to pay player's fines (for obvious reasons), but why would it not allow a third-party?