The first time Kaepernick did it, another guy did it with him. That other guy recently gave an interview and said they did the half knee exactly so it would not be construed as anti-military. Today's USA Today mentions some of this in a feature today. I didn't read it all, but it might be worth a look.
It's odd, to me, that so many people directly tie our flag to the military instead of to the country as a whole.
I know a guy, a good friend actually, who was engaged to a girl back around 1980. The girl refused to stand for the anthem. He worked for the feds as a high-ranking auditor, and he just couldn't deal with it. They broke up because of it. He asked me at the time what I thought, and I said that I thought it was a crazy thing to break up over.