The Flag of the United States is a symbol of the United States. There is an unofficial flag code that says you should stand for the flag as it passes by. There is also a request that you stand during our national anthem. None of these are laws. Not doing so is, perhaps, rude. To some, it's disrespectful to the anthem (or the flag).
I served in the US Army (and reserves) for 12 years (the vast majority of that was reserve time, full disclosure). One reason I did so was to help pay for school, but the other, the more important is that my family (and I) have deep and long-standing feelings that this experiment, this democratic example, represented something special. It represented a nation committed to protecting the rights of those who were unpopular, a nation committed to making sure people were represented without restriction, were free to speak, free to vote, and where they could grow up believing the government acted, in general, with good purpose to protect everyone and pursue democracy FOR everyone, regardless of race, or religion, or ethnicity, or creed. One which, the vast majority of time, acted with integrity because WE, Americans, for the most part, did so, and expected nothing less from our government. I felt that was honorable and something to be preserved, even at the cost of life, even my life, if needed.
The foundation of that system of government was a Constitution which was elegant in it's simplicity, yet rich in meaning. There were letters and words which constructed the stated rights, but more importantly, there were ideas behind the words which expressed an intent. That intent may have been more (or less) limited due to the age in which the words were drafted, but equally clearly, the drafters expected views to evolve. They expected not just that the document might be altered to adjust to the times, but that the understanding and application of the words would evolve. That's not a point for debate, they said exactly such, especially Jefferson who did much of the authoring.
A fundamental protection which ensures the preservation of that democracy, that ideal, is that people have the right to protest without fear of reprisal by the government. Reprisal doesn't have to take the form of overt use of force against those who are dissenting from an action by the government to be sinister and effective in shutting down dissent. Putting people on black-lists, saying they should never be able to work in their field again (as Joe McCarthy requested) is tremendously effective in shutting down the voices of others who might have spoken out against the government. Saying the employer should turn over the comments which employees make in private, on social media, to the government and then having some governmental representative request some sort of reprisal by the employer, would have the same effect.
In the case of the President of the United States asking employers to fire those who do not agree with his opinion about the "flag code" would, equally, have the same effect. It will, if he were effective, would result in those who would otherwise want to protest anything, refrain from doing so. In fact, we've seen that effect with Colin Kapernick. Capernick was a moderately capable NFL QB who was the first to show his displeasure with the state of policing in the US by declining to stand during the playing of our national anthem. His employers, NFL owners, decided to act against Capernick, by failing to continue to employ him. They said it was due to his lack of talent, and that may be part of the reason, but when others, others who were clearly talented enough to be employed, chose to do so, the owners were put in a bind, either fire those (or suspend those) who were speaking out (and potentially embarrassing the NFS in the owners' minds), or, as they have done, acknowledge their employees often come from a rough background, and in some cases, the neighborhoods they grew up in, and the neighbors they still know and love, might be being subjected to profoundly unfair treatment by the police (and by the courts), and so, by the government. So, they were using the form available, the forum MOST likely to reach people, to protest.
We can argue whether they should do so, but we CANNOT/MUST not shy away from the reality that it is not the government's place to act against them. If we want to maintain our democratic institutions, we have to push back on the government when it starts acting to squelch dissent.
So, to me, it's FAR more important to stand up for people's right to speak out than it is to worry about wrapping ourselves in a symbol (a flag) or an anthem. Those symbols pale to irrelevance next to the value we embrace and preserve when we stand up for people's rights to protest, and stand up and speak out against an unfair (or even brutal) system which we, the people, have allowed to develop in response to our fears. Freedom is often a balancing act of weighing our individual safety against the rights of other individuals to act as they chose. Freedom is rarely ever needing to choose between individual rights and the trappings of nationalism. That choice is normally only required in states which lack freedom, in totalitarian states. Mr. Trump is asking our citizens to boycott the business where people are protesting brutality. While I'd embrace Mr. Trump's right to do so if he were a private citizen, once he becomes President, it instead looks like the government seeking to limit speech and in specific, Mr. Trump looks to be squelching dissent about himself.
Standing up for the rights of those with whom we disagree is, therefore, to me the far greater respect for our flag and our country and our ideals than any number of people standing up when a song is song will ever provide.