Essentially, I think that companies & teams would be wise in letting their employees/players know what causes they deem as being acceptable or not, and the employees can decide if that is a type of company they want to work for. Many times I see companies praise the idea of protesting a certain idea, although controversial (at least I've seen it where I am at). It's almost encouraged at times, with many people getting positive visibility for their cause. It seems kinda lame to support one controversial cause and fire someone for supporting another controversial cause.
I would certainly counter the idea that Kaepernick was fired because of his protests though. I think the niners are down with him because he sucks at football now.