Apparently the 49ers are ok with it.
" The 49ers issued a statement before Kaepernick's comments to NFL media were published, saying: "The national anthem is and always will be a special part of the pre-game ceremony. It is an opportunity to honor our country and reflect on the great liberties we are afforded as its citizens. In respecting such American principles as freedom of religion and freedom of expression, we recognize the right of an individual to choose and participate, or not, in our celebration of the national anthem."
The NFL released a statement on Kaepernick's decision not to stand, saying: "Players are encouraged but not required to stand during the playing of the National Anthem."