Kaepernick has said he stands by his decision to boycott the National Anthem and will continue to sit-out future performances.
The Niners quarterback says it's his way of protesting the way blacks are treated in America. "This is because I'm seeing things happen to people who don't have a voice. People who don't have a platform to talk and have their voices heard and affect change," Kaepernick said.
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Kelly said when Kaepernick is at the games, he's all about football.
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Kaepernick took part in warming up with the team on the practice field next to Levi's Stadium Tuesday.
While he hasn't been the focus of the offense this preseason with only throwing six passes in his only game against the Green Bay Packers last week, Kaepernick has been getting a lot of attention for his protest during the National Anthem.
His head coach said it hasn't been a distraction for the team. "They're focused on the 2016 season and how good a team the San Francisco 49ers can be. And I think that we've said all along we've recognized his right to express his feelings, but that doesn't affect what we do when we get here at 8:15 a.m. until we leave here at 8 p.m.," Kelly said.
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Kelly said the team held a players only meeting and it appeared to go well.
Many players have spoken out in support of Kaepernick.
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Others have been critical of the focus of the protest, racism and police brutality.
The San Francisco Police Union sent a letter to the 49ers and NFL, saying they won't stand by as he attacks police officers.
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And the Alameda County Sheriff's Office invited Kaepernick to attend it's police academy.
As for the football field, Kelly said Kaepernick will play this Thursday against the Chargers and called him one of his two best quarterbacks on the team.
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#49ers coach Chip Kelly hasn't talked to Colin Kaepernick about protest during national anthem. He says "it's his right as a citizen."— Matt Keller (@MattKellerABC7) August 30, 2016