This had nothing to do with the military. Here was Kaep's statement on why he was doing it: 

"SANTA CLARA, Calif. -- San Francisco 49ers quarterback Colin Kaepernick has willingly immersed himself into controversy by refusing to stand for the playing of the national anthem in protest of what he deems are wrongdoings against African Americans and minorities in the United States...

"I am not going to stand up to show pride in a flag for a country that oppresses black people and people of color," Kaepernick told NFL Media in an exclusive interview after the game. "To me, this is bigger than football and it would be selfish on my part to look the other way. There are bodies in the street and people getting paid leave and getting away with murder."

Definitely don't want to beat a dead horse, just thought it important to be clear on the reason, whether we agree with him or not. I do think people conflated what he did with inferences and assumptions about the military, but it's not true.