Kaepernick was free to protest. His mistake was doing it on company time. When the customers (eg., fans) decided they didn't like it and boycotted games or went elsewhere, that's their right. Kaepernick's employer was also free to say "Don't do it on my time, do it on your own time." Nothing wrong in any of that.
Actions have consequences. If you are passionate enough about your beliefs, then you should be willing to suffer the consequences that may attend them.