Very interesting thread. Lots of valid points on here, both from the business and private seller point of views.
As a guy who occasionally sells parts that I don't have a need for, I've had interesting experiences with shipping.
First off, as others have mentioned, the cost of packaging. Sure, if I'm sending you some hubcaps, I can probably find a box and some paper without any cost. But if I'm sending a steering column, I need to go buy a box that will fit the column. Then, if you don't want the column to punch through the box or get damaged in transit, I need to bubble wrap the ends and pad the column. That's an additional cost. Depending on the size and shape of the item, that could be $5-$15 in shipping materials before it even gets on a truck. I don't charge for my time, or the gas it takes me to get those three shipping quotes from three different locations, but I do charge actual cost for shipping and shipping materials. Otherwise, it's just coming out of the money I got from selling it in the first place.
Second, packaging itself. Have you ever received a package that had the box ripped open and parts damaged/missing? I have. Usually because the (private) shipper stuffed the part into whatever box he had lying around, regardless of if the part truly fit or not. I'd rather pay an extra $5-$10 for shipping, and get the part in good condition, than cheap out on shipping and have a damaged product.
Third, as has been mentioned, distance. It costs more to ship a part cross country than it does to ship it to the next state/province. That's regardless of size and weight. Most people are highly unrealistic on their shipping costs because they don't factor in where it's being shipped from.
Fourth, some companies have multiple shipping options. The standard seems to be UPS/FedEx 'quick' ship. That's so you get your part in a hurry. But then again, getting it quick means you'll pay more.
Fifth, availability. Is the same part available from a closer distributor/location? You might find that your local parts house charges more up front for the part, but it works out cheaper because there is no shipping involved. If it's not available anywhere else, then I guess you need to either suck it up and pay the shipping costs, or do without.
Whether the seller is private or a company, nobody is out to lose money. Some (most) are fair. Others will gouge. But at the end of the day, the seller has the ball in their court...for better or for worse.