the most recent shooting of a black suspect in SC just brought home the reality that blacks are, in fact, still mistreated in our society (i.e. if a police officer can empty his revolver into a fleeing suspect and feel "justified", then there is something bad wrong).
that was pure murder, and I cringed as I watched and realized what just happened.
back to your original question, "why are African Americans treated so badly in America" -
ultimately, it could be the age-old "tribal" factor at play, if so, the logical solution would be better integration.