As far as I'm concerned, a salute to the flag (or anthem) is to patriotism as a firefighter uniform is to being a firefighter. A firefighter does not need the uniform to be who he is, and the uniform does not make one a firefighter. Likewise, a patriot needs no flag or anthem to be who he is, and all the flags and anthems in the world will never make someone a patriot.
Taking a stand (or taking a knee) to protest injustice in your country, to denounce a betrayal of the country's ideal, is far more patriotic, and far more respectful to those men and women who fought and sacrificed (including their lives) to build that country, to protect it, and to make those ideals a reality, than the blind jingoistic adherence to worship of symbols.