Believe it or not, I'm actually not outraged by his refusal to stand during the Anthem.
If he wants to use that as a form of protest, that's fine. There shouldn't be required patriotism in this country.
However, I take more issue with him doing this while being paid millions to play football. Freedom of speech does NOT exist at work. This is what idiots like Daniel Colman and Olivier Busquet didn't understand when they wanted to wear "FREE PALESTINE" shirts on televised final tables, and Pokerstars told them they couldn't. Private companies have the right to establish a code of behavior at work, and that includes suppressing your speech if they feel it will upset customers or co-workers.
If the 49ers were okay with it, I guess it's fine that he did it, but I also think it was stupid and counterproductive. Honestly, the Niners should have a rule against doing things like this because it's disruptive and can hurt their brand.
These spoiled brats being paid millions per year need to understand that they are partially being paid that much to represent their team in a positive fashion. If they cannot bring themselves to do that, they should quit their high-profile position and go work a regular, low-visibility, 5-figure-paying job like most other people in this country, and then they can do all the protesting they want in their spare time. When you accept big money to represent a major sports team, keeping your obnoxious actions in check comes with the territory, especially if you're not all that good of a player in the first place.