Blacks are harassed and discriminated against many more times than Whites. Whites are generally not subjected to the same level of scrutiny while driving, crossing the border, walking along the streets, etc. 

The Star Spangled Banner symbolizes America, and represents all of the institutions it stands for such as the government, military, justice system, etc. Hence, Blacks have a right to protest these injustices during the playing of the National anthem. They are rightly disagreeing with the elements that the anthem represents.