A portion of the trade value from the goods that pass through the area gets added to the owner's treasury, maybe. If you could set the taxation value, then adjusting it would determine the volume of trade that passes through the area - too high of taxes and merchants will prefer to take the long route.
I just hope rivers will play a major role in trade. It was a national goal of Denmark to gain control over the river outlets from Germany, so they could have full control over trade.