I don't disagree that there is a likely (especially in some places) a systemic police brutality or at least heavy-handed approach. I don't know how widespread. Probably a small minority of cops create a large majority of the problems.
And that needs to be rectified at the local level. Just like Mr. Obama said in his article.
I also believe that there a small minority of police officers who either already are prejudiced or have developed an unhealthy prejudice as a result of doing their jobs.
Because let's face it, if you get a job policing an inner city predominantly African-American community and you are not African-American, you are going to have many opportunities to develop prejudice. The obvious reason is that you are going to deal with the worst people from the community on a regular basis. It would work the same if a black police officer was assigned to work a rural, low-income white neighborhood. It's natural to start building a stereotype in your mind. In fact, it might be a self-preservation tactic.
I think one path to a solution (which once again has to be developed at the local level) is that the police need to do more in the communities than just enforce the law. If there was some community involvement it would create a trust between the police and the community. This would cause the interactions between officers and law breakers to maybe not start out with such animosity. If you knew the officer's first name and he knew yours because you had been in the community you'd be a lot less likely to have negative interaction during a traffic stop.