Yep, that's true, and eBay does it very well. I've sold over 1000 items there and the shipping calculation system is excellent. It allows the seller and buyer see the price in the listing. and, the seller can add handling charges when setting up the listing.
FYI, the calculator is available, without listing here:
http://www.ebay.com/shp/Calculator
It always works for me, just be sure weights and dimensions are accurate.
Grizzly still has the mail order catalog philosophy of charging for shipping. To make ordering easier before the Internet catalogs often had standard shipping rates based strictly on the total dollar value of the order. Grizzly's shipping rates are listed at http://www.grizzly.com/shipping The customer comes out way ahead if they order something that is cheap and very heavy. The customer doesn't make out so well if they order something that is expensive and very light.
There are hundreds or thousands of online stores that calculate shipping costs based on the weight of the item and the distance the item has to travel. It is somewhat rare to find a website that still bases shipping costs strictly on dollar value of the order. When adding a new item to the online store it isn't that hard to add the weight and possibly the dimensions for calculating shipping.