Who buys NIKE gears ? Young and Millenials
Politically speaking, where are Millenials and Youngs ? On the Left
Nike is a huge coorporations and the US is crucial market for them so if they choosed to side on Kaepernick's side, it's for business reasons, not political reasons. Nike's accountants have determined that supporting Kaepernick would earn the money, much more than the backlash would cost them. They've determined that Liberals have won the culture war.
Nike's an important advertiser, they control the real money so when they say that Kaepernick is their guy, the NFL will bow its head. Kaepernick is gonna be back in the NFL