Betsy Ross' 13-star pattern was used as early as 1777 and is associated with the Revolutionary War. In addition, the flag has been appropriated by the white nationalist group Identity Evropa and the Ku Klux Klan, whose members use it to represent a time when slavery was legal.
Kaepernick, a brand ambassador with Nike, was concerned because the shoe design incorporates the flag, which has been adopted by White Nationalists and Racists, as a symbol of glorifying enslaving African Americans. https://www.nbcnews.com/politics/politics-news/arizona-gov-ducey-has-change-heart-nike-following-betsy-ross-n1029241