I'm not really sure why we're talking about rights, here. Of course you have a right to protest in whatever way you want, although many of us wouldn't be given sponsorship opportunities and have lots of defenders if we used the prestige of our employers to make political points that were important to us personally.
When it comes to kneeling or whatever to take exception to the display of the nation's symbols, the people who have a problem with it don't necessarily think the nation is perfect, either. In fact, they probably think many things should change, and that unjust things have been done with the imprimatur of the United States. However, rather than thinking that means they can't respect the country, they work within the system to change things for the better because they believe the nation's ideals are just. That's the difference between a mindset of reform and a mindset of radicalism.
If you have any doubt about what the kneeling was meant to show, just look at Colin Kaepernick's quote about why he was doing it:
“I am not going to stand up to show pride in a flag for a country that oppresses Black people and people of color. To me, this is bigger than football and it would be selfish on my part to look the other way. There are bodies in the street and people getting paid leave and getting away with murder. …
“This is not something that I am going to run by anybody,” he said. “I am not looking for approval. I have to stand up for people that are oppressed. … If they take football away, my endorsements from me, I know that I stood up for what is right.”
Now, not only is that a radical stance, it's also just plain wrong in its reference to police violence against black people. It's woefully wrong about where the major threats to black people's safety come from. But that specific purpose of Kaepernick's protest was subsumed under the more anodyne justification that it was just about general racial inequality. Since that's a good cause, we should ignore the specific symbolism of the protest and what Kaepernick actually said. Let's also not forget about the pig/police socks that Kaepernick wore.
To me, those are all good reasons not to support Kaepernick's kneeling for the anthem and the flag movement. No, the government shouldn't infringe on his right to lead that movement, but people shouldn't feel like they have to support it just because they support racial equality.