Most sites lump their shipping and handling charges into one fee but don't list it as such.There are a number of factors that contribute to the extra handling costs the most significant being direct labor and materials. The stores have to pay someone to pick, pack and ship your order. I would venture to a guess a ratio of 1 man hour per 20 orders. Paying someone $7/hr it works out to $.35/order in direct labor costs. Add in the cost of the box and packing material if it's not the free stuff from the USPS or FedEx. That can easily be an additional $.10.
There are processing fees involved with doing credit card transactions over the internet. The transaction fees for a typical order can be in the range of $.30 - $.65 depending on the processor and transaction features used. (That doesn't include the % paid to the credit card company. Usually on the order of 2.5% of the total order.)
If you're talking international orders then there's a bunch of additional direct labor involved especially if the store does special packaging. There's more paperwork involved in preparing an international shipment. The labor rate of orders easily drops by 50% (or more) to 10 orders per man hour. ($.70/order direct labor cost)
In CA a retailer must charge sales tax on shipping and handling charges for orders shipping within the state. If the retailer lists their shipping and handling charges as two seperate items on the invoice, and they pass through their shipping costs with no markup they are only required to collect sales tax on the handling charges. (I don't know of any sites that list these items seperately.)
A retailer has to build in a cost factor for lost shipments, fraud and damaged items. Some retailers incorporate this into the pricing of their product, others factor it into their shipping charges.
All of these miscellaneous charges add up real quickly. If they aren't built into the cost of the order somewhere they can easily erode profit margins by 4% - 7% on a $20 item.
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