Its normal since they need to send somebody to pick up the car and return it to Amman.
Almost all rent a car companies are having such a Surcharge when you leave the car in other city.
If you are talking about one way, or one day, its might be better for you to look for a driver with his car.
If you are renting the car for few days, then it might be justified.
Enjoy your trip.
This "one way" fee is a normal thing, not just in Jordan. And it's indeed the cost to have the car returned back to the original location.
Patricia (Petra Bed Breakfast - Horse Riding Jordan)
Thanks for the reply. I did not realize that is the one-way fee. I thought it was something related to the border.