How do you know he's never done it before? Think about it--do you think that you're the first cyclist he ever threw something at? I don't. Asshats like this don't change, and a "lecture" from someone in uniform, or even wearing a black robe, without any other consequences, reinforces the idea that no one takes it seriously in their minds.
Filing charges, on the other hand, takes the matter out of your hands, at least in part. Unless you're in a small town, where everyone knows everyone, a cop isn't likely to just give a guy a "talking to" if you file a report. They'll go out and either arrest him or issue him a court summons. If a complaint is issued and the guy has to go to court, you're not longer the one bringing charges. It's the prosecuting agency in your state, and while they will listen to you, it's not automatic that they'll let you drop the charges in return for a "lecture" from the judge. I agree that it's unlikely he'll go to jail unless he has a record from here to the door. He may even keep his record clean, or at least avoid a felony conviction, assuming that assault or A&B with a dangerous weapon is a felony where you live. But IMO you owe it to both yourself and other riders to file the report and let the chips fall where they may.