Just two days before, Kaepernick had shared a photo on Twitter of himself featured in Nike's new marketing campaign, which is tied to the 30th anniversary of its iconic "Just Do It" tagline. Due to Kaepernick's activism, the news quickly went viral, pulling waves of both support and backlash. #NikeBoycott was trending on Twitter by Tuesday morning, and Nike shares were falling as Wall Street reacted to the news.

Kaepernick flew into the spotlight when, to protest racial injustice, he decided to kneel rather than stand for the national anthem before a 2016 National Football League preseason game. He's not currently signed with an NFL team and has since charged that the organization conspired to prevent him from getting signed to a team when he became a free agent. The NFL denies his allegation. A hearing is expected on the matter before the end of the year.

Despite Kaepernick's appearance in it, the new Nike commercial isn't overtly political. It makes no reference to "taking a knee." Instead, it sticks to the inspirational tone that Nike's "Just Do It" campaign is famous for.

Kaepernick, the narrator in the video, starts by saying: "If people say your dreams are crazy, if they laugh at what you think you can do — good, stay that way, because what nonbelievers fail to understand is that calling a dream crazy is not an insult, it's a compliment."

The video runs through images of professional athletes such as Williams and James before their sports careers really took off, when they were still in their youth. The roughly two-minute clip ends with Kaepernick saying: "So don't ask if your dreams are crazy. Ask if they're crazy enough."

Nike said the ad will be shown Thursday when the NFL season kicks off with the Atlanta Falcons taking on the Super Bowl champion Philadelphia Eagles. It also will air during other sporting events such as the U.S. Open, Major League Baseball games, and college football.

Comments have flooded the internet since the campaign featuring Kaepernick was announced Monday. Some industry analysts expect Nike to win over consumers who are more sympathetic to Kaepernick's cause. However, there have been numerous images of people burning their Nike shoes posted to Twitter, along with pledges to never buy Nike products again.

"When you are an extraordinary brand you are going to be polarizing," Allen Adamson, brand expert and co-founder of marketing solutions business Metaforce, told CNBC. "There's going to be some short-term bumpiness because of this campaign, but the best brands need to manage for the long term."

President Donald Trump later tweeted about the partnership and reaction on social media, saying: "Nike is getting absolutely killed with anger and boycotts. I wonder if they had any idea that it would be this way?"

tweet

Although Nike shares shed 3 percent on Tuesday, the stock is up more than 50 percent over the past year. On Wednesday the shares closed up less than 1 percent.

Still, in a less-than-24-hour window, one group estimates Nike already received more than $43 million worth of media exposure, much of that positive.

"Right now what this means is they are winning the battle from the public relations side," Eric Smallwood, president of Apex Marketing Group, which measured the branding exposure for Nike's new campaign, told CNBC.

Analysts also argued that Nike's target audience of consumers stretches far outside of the U.S. and that many shoppers globally won't be paying much attention to the Kaepernick tie-up. Further, the retailer is aiming to connect with a younger generation that puts more thought into what their favorite brands stand for before they make purchases.

"Most people aren't looking to make political decisions with their sneaker purchases," Nomura analyst Simeon Siegel said. "But whenever a brand attaches its logo to someone else's face, they are making a calculated cost benefit analysis that is something that has been core to Nike's DNA."