Amazon does makes a decent margin above the marginal cost of the $299 kindle fire HD and on the kindle fire HD LTE: http://www.eetimes.com/electronics-blogs/other/4395833/BOM-b...
It's hard to tell if they profit even after including fixed costs, but they might.
But pricing it's low end model slightly above it's BOM is a signal to competitors: "we don't care to profit from sales, if you'll compete, you'll lose".