How much would it cost you to go pick it up? It costs the carrier money to transport items. And that cost eventually gets conveyed to you.
Cost of shipping an item isn't based on the cost of the item. In part it's based on the weight and size of the package. Also some shippers include the handling (carton, packing, insurance and labor) charge as part of the shipping.
Working for a carrier I hear it all the time; why does it cost so %*@% much to ship a little box. My standard answer is above.
I have to agree, you shouldn't have be charged shipping on a back ordered item. When I was in the HVAC wholesale biz, we ate the shipping on back ordered items to keep our customers happy.