It's all about symbolism, Amber. The same reason statues are being torn down. 
Kaepernick choose the one symbol that represents ALL Americans, and with his own words ("for a *country* that oppresses") he condemns ALL of America as being racist and unjust. That is a talking point currently being used to divide this nation. 

And this coming from the same guy who praised Castro, a vile dictator who treated his people far worse than racism. So Kaepernick's rather consistent with his anti-America views. 
Makes me wonder why he bothers to stay in a country he obviously hates.