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I don't know what Amazon pays, but there is a per-purchase fee on credit cards. Depending on the merchant and the goods and other factors it can be anywhere from 11 cents to sixty cents. This can cut the Amazon fee's in half.
Furthermore, I suspect that Amazon has significant marketing fees. Go to the current best seller list and you will find a book listed as a hard cover for $27.95 and sold as a hard cover for $16.77 (with free shipping on orders over $25) and sold as a Kindle edition for $9.99.
I imagine that Amazon is making a loss on best-selling hardcovers, especially when they have to throw in free shipping. They may be losing as much or more on the Kindle editions of best-sellers.
These losses would be marketing expenses that are used to attract buyers to their store. Now, they have to make up the losses on sales of non-NYT bestsellers. This means that these small books must make up enough profit to cover the deals on the best sellers, and since there are a lot of best-sellers sold, this gives them a lot to make up.
Why should a small book seller pay for discounts on big books? Well, the reason the small book seller wants to sell on Amazon is because Amazon has customers. The reason they have customers is because of their cheap prices. So, the little guys have to pay for the access that they want.
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