Unfortunately, all the police need to charge someone with a crime is probable cause -- a reasonable belief that your son may have been involved in criminal activity. It is reasonable -- though not necessarily true -- for the police to believe that if your son was with someone who committed a murder, he was part of the criminal enterprise. This, and the felony murder law of your state would allow the police to charge your son as a co-defendant even if he was not the person who had the gun or who actually committed the act.
He may have just been at the wrong place at the wrong time. In order to convict your son, the state has to prove its case against him beyond a reasonable doubt, and during the course of the case, your son's lawyer would be entitled to a hearing to challenge the basis for the stop, the arrest of your son, and the possible bias of the detective. But at this juncture, the state is entitled to try to prove the case against your son. That means he needs legal assistance.
Some public defenders are excellent attorneys. As would apply to any other group of lawyers, public or private, some are not so good and most are at least average. All public defenders have substantial experience, because criminal law is all they do for a living and they have heavy caseloads. Hopefully. he has one of the good ones. For additional support, you can contact your local branch of the NAACP and also contact the American Civil Liberties Union. They also have branches all over the country. Both organizations advocate on behalf of civil rights and may be able to direct you to a local criminal and civil rights lawyer who does pro bono work, and see to it that your son's rights are being honored while he is in custody.
Down the road, if it is found that his arrest was, in fact, motivated only by his race and that his arrest was unlawful, he would be able to bring a civil right suit against the police. Right now, however, the matter hasn't been litigated. And that's the first step to determining his innocence.