The president's son posted his own version of the ad on Instagram Wednesday with the comment, "There, fixed it for you".
"In their new ad campaign, we believe Nike executives are promoting an attitude of division and disrespect toward America", said College of the Ozarks President Jerry C. Davis.
Kaepernick tweeted the two-minute ad Wednesday morning.
Kaepernick already had a deal with Nike that was set to expire, but it was renegotiated into a multiyear agreement to make him one of the faces of Nike's 30th anniversary "Just Do It" campaign, according to a person familiar with the situation who spoke on condition of anonymity because details of the detail had not been revealed publicly.
Kaepernick, a former San Francisco 49ers quarterback, has developed into one of America's most polarizing athletes the past three years because he juxtaposed social commentary with sports.
"I am sponsored by Nike", Funchess said.
"I think people in general have to get more politically involved".
"Having a huge company back him could be a controversial reason for this company but they're not afraid and I feel like that was a really powerful statement to a lot of, a lot of other companies", Williams said.
Kaepernick, a former quarterback with the San Francisco 49ers, rose to prominence after electing to kneel during the U.S. national anthem to protest racial injustice.
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"Nike has always had athletes that were on the cutting edge", said Dick Dillard with Fast Break Athletics.
He also said, "As much as I disagree with the Colin Kaepernick endorsement, in another way - I mean, I wouldn't have done it, in another way, it is what this country is all about, that you have certain freedoms to do things that other people think you shouldn't do, but I personally am on a different side of it".
Nike is the official uniform maker for the NFL. He has since filed a grievance with the league accusing owners of colluding to keep him off the field.
Newton said last season he thought the way Kaepernick has been treated was, "unfair", and when asked his thoughts on the new Nike campaign, Newton doubled down in his support.
The ad is also expected to air this week during college football and Major League Baseball games, and stream on various music, gaming and other platforms, Nike spokeswoman Sandra Carreon-John said.
Newton said Kaepernick has his respect. Kaepernick said he was protesting police brutality.