I don't know if publishers manage to get better deals from Amazon, but Amazon's Kindle Direct Publishing has an annoying aspect that the ebook royalty rate falls from 70% to 30% after $9.99, which gets very awkward for a tech book you'd like to sell for, say, $19.99.

Also, piracy is rampant and Amazon doesn't do much about it. Publishers have more resources to stay on top of it, I suspect.