The idea that the flag or the anthem stand for freedom and liberty is a nice one, but one that falls on its face when it's only for approved freedoms and liberties. The right to dissent or protest is even more important than the right to simply go along with the rest of the stadium. Anyone can do that; it take guts to decide not to do the (ahem) politically correct thing.
Now, to play devil's advocate, one should also note that if Kaepernick is trying to start a "conversation" or a "dialogue," there were and are any number of better ways to go about that. He is, after all, an NFL quarterback who came within thirty seconds and a dropped pass from winning a Super Bowl just a few years ago. Any number of reputable Bay Area journalists would have been happy to sit down and interview him, if he wanted to start a discussion on race. Performing provocative stunts like wearing socks with pigs wearing police caps, or pointedly sitting down through the national anthem, tend to (you'll be surprised to find) provoke something other than reasoned discourse.
There is also the workplace aspect of this particular protest; Kaepernick is a contracted employee of the San Francisco 49ers, and as such is subject to all sorts of expectations, some you might assume, some you might not. For example, he probably is contractually forbidden from riding a motorcycle, or perhaps even playing a pickup game of basketball. He is also most likely prohibited from doing or saying anything that might reflect poorly on the team organization, so if he (for example) posted a racist tweet, the Niners could cut him loose without losing anything beyond guaranteed money (and maybe not even that).
Most of us have jobs where we can say what we want outside the workplace, but cannot exercise absolute free speech on company time. Again, see "racist tweet" example above. A place of business is under no obligation to accommodate the beliefs and opinions of its workers. Kaepernick has probably tread very close to that fine line; at the very least, especially given his demotion, it would surprise no one if he were traded in the next few days to a team that needs a quarterback (I'm guessing Denver, if there's a deal to be had).
All that said, what Kaepernick has done and said may be offensive to the more sensitive internet tough-guys out there, but the fact is that it neither picks anyone's pocket nor breaks their arm. He is, people should keep in mind, only twenty-eight years old. I'm sure none of us ever did or said anything we later regretted, or at least wished we could have done better and more clearly, when we were in our twenties.
Professional sporting events and their participants occupy a strange limbic place in the collective American psyche. Where some of us simply watch sports to see an exciting competition between people who can do wondrous things, clearly there is a large swath of folks who see sports as a broader, deeper affirmation of their society and their relationship to it. They need the overt nationalism, the cheap jingoism, the politically correct respect for authoritah.
These are the same people who destroyed their Dixie Chicks CDs a decade ago, who won't watch any movie with an actor that has spoken their mind in a way that they disagree with, etc. They really don't seem to get that their stance is simply the right-winger version of the political correctness they profess to despise, but that's exactly what it is.
As long it doesn't hurt anyone else, it is every American's right to be wrong, and even to be an asshole about it. I might not like your confederate flag or what it really stands for, but I don't have the right to keep you from flying it on your house or car. (Public spaces are another matter, which would seem to be obvious, even to these troglodytes, but of course it needs to be explained to them every goddamned time.)
A professional athlete has a free-speech right (although there's no guarantee to a workplace right) to sit out the forced, joyless anthem ritual, something everyone at home switches away from or hustles off to get a beer or take a leak during anyway. Without the right to dissent or refuse to participate, we have nothing, people have fought and died for nothing. It's pathetic that these would-be enforcers of right-wing PC can't see that. It's just another bullshit hot-take for some of them to cynically pad their tape when they pack up their kneepads and head (forgive the pun) over to Fox.