Well, the alternative that port authorities use nowadays is not allowing the ship to unload its cargo. Due to the nature of the game, this is not possible. Shooting, however, is.
I think this is protectionism in a way, and I'll be watching to see what the reaction of most traders is. The low levels of levies imposed might be a good idea to provide some sort of revenue for naval and police factions outside trading on alternate characters, but Im doubtful it will be recieved at-all well from transport pilots.
Alternatively, people will just find trade routes with places that the RM never are but are still in Rheinland. At least, that's what I'd do.