VAT on ebooks for a start.
Plus, certainly for a while, not sure if it's still happeneing, the publisher sets the price not Amazon. Thanks for that Apple...
It beats the alternative - at one point Amazon wanted to have the ability to set book prices, completely for ebooks (as in if a publisher wanted to sell books on the Kindle, Amazon got to set the price at whatever they wanted, pay the publisher what they wanted*, and the publisher couldn't let anyone sell the book cheaper elsewhere, even if the other seller decided to make a loss).
Basically Amazon tried for a monopoly on the distribution and sale of ebooks.
The publishers looked at Apple's version of the system (as they were the biggest competitor) and that one was closer to one that could work...
IIRC the most of the publishers didn't fight the case in America not because they were guilty, but because the costs involved in fighting it could have driven them to bankruptcy (especially as apparently under the practice of the US authorities in such cases, if say 4 companies are charged, and 3 settle, the remaining one is liable for all costs and any financial punishments that would have been applied to all 4).
Publishers don't tend to have the spare hundreds of millions lying around to fight complex legal cases - not least because they're unable to use many of the tax dodges some companies do
IIRC most ebooks follow the same sort of pricing as paper ones for new releases because, to put it simply, the cost of doing an ebook (once you allow for the fact there is VAT involved in them, but not paper ones) isn't too different to the costs for paper books.
To get an ebook version looking right can often require the publisher to go through the page layouts separately for the ebook versions - something for a while Amazon from memory tried to do automatically much to the annoyance of the publishers who ended up with the complaints about "why does this look like a load of rubbish".
Back slightly more on topic, Amazon will be the ones setting prices for the kindle versions, and can if they want sell for under the wholesale cost if they wanted (same as they can and do, for paper books).
*I can't remember the figures, but apparently at one point Amazon only wanted to pay the publishers some much smaller amount per book than was normal under paper versions - which would have seriously screwed most publishers (for whom only something like half their books break even, and an even smaller number make a good profit).
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