the crime is deprivation of rights "under color of law"; the ordinary rapist doesn't have the force of the state behind him. A judge or prosecutor or sheriff who does it in apparent connection with official duty does. Or the sheriff who beats you to death (see a case from the 1940s in the Supreme Court, US v. Screws)(Yes, the sheriff's name really was Screws!)
That's what the Feds prosecuted him for, alright--not for rape. It's just like I said--the state made a weak effort to prosecute the rape charges so the Feds stepped in and prosecuted the case as a civil rights violation.