It could actually be that Nike figures much of its customer base would be sympathetic to Kaepernick. I don't really know, not keeping up with team sports stuff that would lead to jersey sales, wearing the same $400 shoes as some basketball player, etc.
However, hitching your wagon to a lightning rod that is currently getting support from the Iranian president and John Brennan? As a business, you might want to take a step back from someone so volatile.