He is free to disagree, and I do not think he is a bad person or a racist for disagreeing. However those he works with , calls friends, or calls fans have every right to challenge his position through discussion, and decide their position on his future in the previously mentioned categories(fan, friend, coworker).
Honestly I think this whole thing blows over (within the team that is) and Brees ends up kneeling in solidarity with the team at some point (likely pre-anthem) before standing during the anthem.