At the risk of repeating myself, the shirt Kaepernick wore was not a Castro shirt or a shirt celebrating the life and career of Castro. It was a Malcolm X meets with Castro in Harlem shirt.
The meeting was in 1960, shortly after the Cuban revolution and before Castro went on to commit the worst of his crimes. At the meeting Castro spoke out against black oppression, this was four years before the Civil Rights Act and still a year before the last documented lynching in the United States, so it should be easy to understand why he was warmly received in Harlem and why the meeting with Malcolm X is still seen as iconic to many in the black community. It had nothing to do with communism. Castro didn’t declare himself a Marxist/Leninist until more that a year later in December 1961.
Kaepernick understood the story behind the meeting depicted on his shirt much better than those who keep repeating the stupid canard that it had anything to do with communism. To Kaepernick the shirt illustrated that more than fifty years ago Malcolm X was inviting foreign leaders to Harlem to speak out against black oppression and yet it still continues, to the extent that he wanted to do his own small part by sitting down while others stand.