In a healthy society, this form of non-violent protest should be allowed, but his employers have their prerogative as well, and they might see this demonstration as something that reflects on them, therefore they may choose to take action based upon his refusal to honor the United States.
I wish Kaepernick himself would elaborate further on just what the fuck his problem is with the country that has provided him the leverage and latitude to be who he is, and if he has, I'd like to hear it.
I personally see this as counter productive to the race issues in America, as we are all Americans here, and furthermore, we are member of the human race, first and foremost. No one segment of society is perfect, let alone the whole, and there are and always will be corrections that can be made. However, simply acknowledging that there is a problem is not enough. We need solutions. Blame-game hot potato does no one any good.
Kaepernick is the American Dream. Perhaps he should focus on that, why that is, and seek to inspire those he feels are disadvantaged. Where there's a Will, there's a Way.
Also, I wonder if the circumstances he feels are hurting the black community are also issues faced by members of other groups? And what are his proposed solutions to the problems he's addressing?