Kaepernick didn't start this, the media and flag jingoists did. He didn't say anything about it before the first time when, instead of standing he remained seated. Nothing was made of it until the third pre-season game and somebody asked him. He answered honestly and after that, the old white men had a conniption. It was completely his right to decide he wasn't going to stand for the flag because he wasn't going to honor a country that in his words:
"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."
After that, he was joined by others, Trump put his big fat ass into the issue, etc.
The 49'ers were bad in his last few starts for them and benching him didn't improve them. The team was bad. Kaep certainly did have some weaknesses but to say he was awful is ludicrous. He took them to the Superbowl his first year and was one interception away from winning it. The next year, he nearly took them back but that interception bug bit him again, although it took a great play by Richard Sherman to stop him.
Fast forward to last year, when nobody signed him. Maybe he wasn't first string material but he sure as hell was better than many back-ups. Has anybody heard of Christian Hackenberg or Brad Kaaya? Kaep wasn't signed because he was not worthy of wearing the jersey as a backup, he wasn't signed because of the controversy that old white men kicked up.
Regarding Nike, the campaign is led with the uplifting message:
"Believe in something. Even if it means sacrificing everything."
Kaep certainly embodies that message. It's also a message to all the old white men who are burning their Nike socks today. Nike are pretty much putting it on the line too, as witnessed by the downward spike in the stock price.