Surely the run-through loses the charge bonus, though?

I use run throughs with Royal Knights (especially the King's) against archers - since they tend to run away, they have their backs to you. And since you didn't official charge them, the unit continues to barge through them, as opposed to attacking. It seems to work especially well with a single row (ideally with the full 20/21 men) - I think this is because the men on the edges continue at full pace, and the ones in the middle struggle harder to catch up.

I almost always use this tactic on the first turn of my Early English campaigns against the French in Normandy - typically, the RKs will wipe out around 25 archers, breaking them instantly (the rest are quickly captured), with only one or two losses to the RKs,typically from missiles on whilst charging as opposed to the combat itself.