Referring to police killings of mostly unarmed black men, Kaepernick's actions angered some members of the Santa Clara, California, police union, who threatened to stop securing Levi's Stadium as long as Kaepernick's actions remained acceptable to the team. (The 49ers have remained neutral.)
Other groups, however, have lauded Kaepernick for putting social issues above football, including his team-mate safety Eric Reid, who knelled during the anthem with Kaepernick on Friday, and soccer standout Megan Rapinoe, who knelled during the anthem on Monday ahead of a game between the Seattle Reign and the Chicago Red Stars.
"We need a more substantive conversation around race relations and the way people of colour are treated," she said after the game.
Even US President Barack Obama has got involved. He told journalists while travelling in China that Kaepernick is "exercising his constitutional right" to sit during the national anthem, while conceding that the protest could be a "tough thing" for military service members to accept.
Kaepernick's actions have offended some military members, but certainly not all. Enough veterans have expressed their support for the quarterback that the hashtag #VeteransforKaepernick trended worldwide on social media late last month.
Kaepernick has promised to donate US$1 million of his earnings to charities that support racial equality.
"I've been very blessed to be in this position and make the kind of money I do," the player, who will make a base salary of US$11.9 million this season with the 49ers, said last week. "I have to help these people.