I believe the profit of enterprises depends on the amount of base resources in the city's goods store, as the cities in this mod don't produse a lot of the base resources, your enterprises will not be very profitable.
You can however buy these recourses elsewhere and hand them over to your whoever commands your enterprise and he will produce the final product out of them. You can also tell him not to sell it, but to keep them in his inventory and you can then try to get better prices in different cities.