The financial hit does however follow an outpouring of criticism from outraged fans who took to social media – threatening boycotts, posting videos and photos of Nike shoes set on fire, swoosh logos cut out of socks – to express their disapproval of Nike's decision to make Kaepernick part of their 30th anniversary "Just Do It" campaign.
The hashtag #NikeBoycott started trending on Twitter, while many others chose to poke fun at the proposed boycott with some even filming satirical videos of themselves destroying fake Nike merchandise.
But some have noted that Nike's decision to delve into politics, and their support of Kaepernick could be a good thing for the company going forward.
Nike's brand vice president Gino Fisanotti said the ad campaign was a way of targeting a new generation of athletes.
"We believe Colin is one of the most inspirational athletes of this generation, who has leveraged the power of sport to help move the world forward," Fisanotti told ESPN.
"We wanted to energise its meaning and introduce 'Just Do It' to a new generation of athletes."
And that strategy seems already be working in some quarters, with Business Insider reporting that millennials were snapping up shares of Nike at 300% more than what they were sellling on the no-fee brokerage Robinhood. There is further evidence to show that younger generations like millennials are driving brands to practice socially responsible marketing.
Brian Gordon, CEO of Engine Shop, a sports and entertainment marketing agency, said the ad is provocative but "authentic to who they are and the communities they represent and speak to," including the athletes.
"Even in the face of potential backlash, they support their athlete partners, and that's an incredibly powerful statement to the athlete community," Gordon said.
Other athletes in the campaign include tennis star Serena Williams, New York Giants wide receiver Odell Beckham Jr. and Shaquem Griffin, a linebacker whose left hand was amputated when he was 4. But the Kaepernick ad struck a nerve, timed just before the NFL season kicks off on Thursday.
"What you stand for is almost as important as what you make," said Allen Adamson, co-founder of marketing firm Metaforce.
"It's a polarised marketplace. No matter what you do, you offend some people. They're focused on what they stand for, and if that upsets some users, so be it."
Robert Passikoff, founder of marketing consultancy Brand Keys, said an ad like Nike's will divide people, but the outrage won't last.
"My guess is that the audience that is reacting so badly to this aren't buying a lot of Nikes anyway," he said.
"They'll move on to the next thing. Welcome to the 21st century."
-with AP