Trump has repeatedly criticized Kaepernick and other NFL players after they started kneeling during the national anthem to protest police brutality and racial inequality.
Nike's ad campaign has galvanized supporters and critics alike on social media.
"Thank you for believing in me, as well as Nike and being able to do this", he said to the crowd.
Kaepernick is unsigned by any NFL team, and is now suing the league for allegedly blackballing him over his protests.
Kaepernick and other prominent athletes who kneel during the anthem have repeatedly said that they do not mean any disrespect to members of the USA military.
"In their new ad campaign, we believe Nike executives are promoting an attitude of division and disrespect toward America", College of the Ozarks President Jerry C. Davis said in a statement explaining their decision to remove all Nike athletic uniforms and gear.
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Meanwhile, Trump is clearly enjoying watching the fallout from Nike's endorsement of the leader of the movement he's enjoyed railing against since it first got going.
"So when Nike did this, it's their right I have nothing against it", said Feed Our Vets founder Rich Synek.
'I honor the flag.
"They feel the same way", Trump said in an interview with Fox & Friends that aired Friday morning.
The NFL season is set to kick off Thursday night on NBC when the defending Super Bowl champion Philadelphia Eagles host the Atlanta Falcons. The league froze the policy after the players' union filed a grievance. "But I think as far as sending a message, I think it's a awful message and a message that shouldn't be sent".
But the league and union put that on hold after the Miami Dolphins faced backlash for classifying the protests as conduct potentially detrimental to the team - putting players at risk of fines or suspensions.