“It was making this whole issue confusing to the fans, to the military, to the players, to the coaches. No one had clarity,” he said."

Really? It was all pretty clear to me. 
By is own words, Kaepernick knew the American flag is the symbol that represents this country and all its citizens: "I am not going to stand up to show pride in a flag for a country that oppresses black people and people of color." He perceives the USA as evil and filled with white racists. Add to that his choice to wear socks depicting police as pigs and his anti-law enforcement, anti-America mentality is clear. 

Thus every player and coach that followed his lead, whether they had different motivations or not, accomplished the same thing: their actions accused the entire population of being evil and full of white racists.
 
None of the empty words now about "showing unity" (you chose the NFL over fans and even pride in your country?) are going to unscramble this particular egg.