The right to Free Speech were initially given to the citizens so they have the power to conduct a protest to government practices/legislations that they're disagree with. This right provide protection for both verbal and non-verbal speech.
Free speech is only prohibited only if you're violating the rights of other people while doing your speech.
Burning the flags is a form of non-verbal speech that's often carried out to protest government practice and none of other people's right were violated during the process.
