One reason why Supreme Court ruled that Chaplains an offer prayers in Congress and in state legislature is that prayers have been offered in those places since colonial times.
Acts of free speech pose critical questions that we as a society need to debate and discuss and address. The protests are meant to make the nation better by raising difficult issues and striving toward solutions.
Unpatriotic acts attack the fabric of the nation and the ties that bind us together. They don't aim at improving us as a society so much as they tear down institutions and relationships that we share.