Kaepernick was fired because of his constant, ignorant (and to be honest racist and anti-American) advocacy which was "bad for business". I'm a strong advocate for free speech but in certain circumstances you have to gauge the room and realize that your actions, even if they seem noble and true... can result in negative consequences. When you're an employee and you're doing something that either hurts the businesses profits or rate of production. You CAN GET FIRED.
It's like if you work at Starbucks (which you probably do) and everyday you wore a tee-shirt that said coffee drinkers are snobby, fake virtue signaling, modern day Hippies. The coffee shop would probably lose business because of you for pissing off the majority of their base customers.