I don't think Amazon is selling most of its Kindle books for "well below what it pays publishers". My impression is that publishers get 35% of the list price (e.g. the price shown at mobipocket.com). Amazon deeply discounts the list price, but not to the point of loosing money in most cases. Like Sony and eReader (now FictionWise), they have the advantage that they are the DRM-provider / wholesaler and so there is one less party to pay.
Note that publishers could break the Amazon Kindle "monopoly" in an instant. All they need to do is stop using DRM. Then they could sell Kindle versions from their own web site (100% of the revenue to the publisher) and the cost of DRM is removed from the picture.
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