Papa Johns courted controversy a year ago after weighing in on the national anthem protest.
While the move was met with widespread praise, it was also greeted with anger by many who see the Kaepernick-initiated protests as disrespectful to the U.S. flag. Kaepernick hasn't played for the 49ers's since 2016 and is suing the National Football League for collusion to keep him from playing.
"Hey Nike I guess you made Kaepernick your new "face" of the brand because you love the way his socks look with your shoes?"
While Kaepernick is receiving support on social media, some critics reacted by destroying Nike gear like sneakers and socks.
Other commentators have noted that Nike, which earned $34.5 billion in annual revenue last financial year, would "be OK" despite the current protests.
Kaepernick triggered a political firestorm for kneeling during the USA national anthemin 2016 to protest racial injustice. Some posted videos of themselves burning Nike shoes and apparel or cutting the swoosh logo off their clothing.
Supporting disruptive athletes has always been a part of Nike's marketing, dating to the early 1970s and runner Steve Prefontaine, the company's first athlete endorser. In subsequent games, he knelt, sparking a movement that other players joined to protest police brutality and social inequities.
"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" said Gino Fisanotti, Nike vice president of brand for North America. In fact, the slogan in the ad could well have been referring to Nike's decision to believe in something-and sacrifice customers and revenue as a result.
Kaepernick received an enthusiastic welcome from fans at the US Open's showcase tennis match between Serena and Venus Williams on Friday night when he was shown raising his fist on the big screen. The former National Football League great Jerry Rice accused Kaepernick of "disrespecting the flag", though he said he understood his stance.