Amazon does subsidize the cost of the books - at this time, Amazon is taking a loss on NYT bestsellers and other 'hardcover' ebooks.
But since Kindle customers are pretty much locked in to the Amazon store, the lower ebook prices for the Kindle are a major selling point. (Until sometime down the road when Amazon has enough customers locked in and raises the prices. Mwahaha)
The Sony offers more freedom of choice. Since Sony doesn't lock you in to any one retailer for DRMed books, that's your trade off.
I'd rather pay a bit more for the freedom of choice myself. YMMV.
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