I propose that Amazon, as an electronic retailer, has chosen to use shipping in place of physical retail space (i.e...they very much have robbed occupancy to pay for shipping). Every retailer must have a distribution network... Amazon choses to own theirs, just as virtually all of the big retail chains in America do. There's no disputing that those costs are real. There's also an economy of scale to them that gives large retailers an advantage over small retailers. Sadly, Walmart didn't kill small-town America -the ability to create complex logistical systems using IT did.
Yes, Amazon has a distribution network that costs money to operate. Investors seem to think they're operating it pretty effectively. Over the last 5 years, their market valuation has gone up by about 4x. Also, as
@Derg points out, they've been able to place a greater percentage of the shipping burden onto the purchaser. I see that trend continuing with nary a peep from consumers.
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To your point though, total shipping costs have risen while oil prices have slacked off. What will happen if oil gets above $100 a barrel? I believe Amazon can weather that storm better than Walmart just based on how their businesses are structured -Amazon is increasingly trying to be a content and cloud business.