This is an emotional issue and doesn't lend itself to logic however; if there seems to be a systemic problem in a country (and that certainly seems to be the case in the US), then it seems very appropriate to protest those issues using symbols of the country like the flag or the anthem.
Those, like Trump, who want to defend the symbols rather than recognize the problems behind the protest show their true colours by doing so. Trump is OK with doing that because he is constantly doing things that appeal to his base of supporters almost to the exclusion of everyone else. In this case, the protest seems to be very respectful. It isn't as if they are burning flags or interrupting the anthem with some kind of chant. It is also interesting that Trump and his supporters supposedly put so much symbolism and importance in the US flag and anthem but don't acknowledge the (negative) symbolism in the Confederate flag and other Confederate symbols. As Trump might say: Sad!