The FREEDOM of Kaepernick to not stand with hand on heart during the playing of the national anthem is exactly what the flag represents.   

And the national anthem is a particularly relevant symbol for his protest of what he perceives as the unfair treatment of people of color in America.  The anthem was written by the slavery supporter Francis Key during the War of 1812.  During that war the British army enticed black slaves to join them in fighting their American masters.  This explains the last four lines of the third verse of the anthem...
 
"No refuge could save the hireling and slave
From the terror of flight, or the gloom of the grave:
And the star-spangled banner in triumph doth wave,
O'er the land of the free and the home of the brave."

"http://www.theroot.com/articles/history/2016/07/star-spangled-bigotry-the-hidden-racist-history-of-the-national-anthem/