So far, there hasn't been much said about the employee/employer obligations and relationships.
I've only worked for 2 employers as an adult. One for 35 years and one for 12 years. It's been my experience that no matter my personal feelings and problems, as an employee, I am a representative of my employer.
Kaepernick is an employee of the 49er's and by extension, the NFL. Unless and until he's a designated spokesperson for either, he needs support and conform to their philosophy. IF he does not want to do that, he's free to seek other employment.
The guy makes 19 Mil a year. What has he done off the field to demonstrate his position?? On the field, he needs to do what his employer expects him to do, represent the team, and win games. He may have a whole lot of time, in the future, to sit or stand, as much as he wants, on his own time.