#1) The problem with protesting during the national anthem is if you had asked people before all of this started what the flag and anthem represented, an overwhelming number of people would have responded that they represent this great country and the people who have sacrificed to make it great.  So by kneeling, regardless of their purpose, it is taken as a slight to the country and those who sacrificed.
#2) It seems to me that they are protesting the RESULT of the problem rather than the ROOT of the problem.  They complain that police are unfairly targeting blacks.  Why?  It could have to do with the fact that blacks only make up 15% of the population in the US but commit over 50% of the crime.  That is an absolutely staggering statistic.  It's human nature to profile when the numbers are that overwhelming.  The ROOT of the problem lies in black neighborhoods where the education system is horrible and jobs are scarce.  That's where the efforts and resources need to be focused.