Can you imagine what would happen if a muggle got bitten? Not only did they not believe in the supernatural before, they now transform every month into a monster and have no idea how to control it. It’s in the ministry’s best interests to keep muggle werewolves under control and away from normal muggles.
That’s a bit circular though. See, if the ministry didn’t do that, then werewolves would not be considered supernatural at all–no more than trees growing are supernatural.