I agree with your points here. The most important point I would like to make is that protests frequently raise issues which make people uncomfortable. Rather than try to consider why people are protesting, many people prefer to use rationality to justify why people should not be protesting. In the case of the NFL protest as you’ve mentioned, people who are against the protest try to reframe it as disrespecting the country by disrespecting the flag.
President Trump has certainly been a leader in trying to shift the focus of attention from the issues of equal justice for all people to you’re a traitor to your country if you don’t stand up for the pledge of allegiance and should be fired from your job.
The rational justifications I listed are all designed to shift the focus from why protesters are protesting to why protesters are wrong to protest without addressing the issue the protesters are trying to raise awareness about. It’s a variation of bait and switch tactics.
Ultimately the comfortable want to remain comfortable and use appeals to rationality to justify why they don’t need to even consider making any changes. The amount of resistance to the protest seems to be a measure of how far we still need to go to establish justice for all in our country.