Give you access to a robust infrastructure that won't crash
Market the site
Build and research a top quality e-Reader
Build data centers all around the world
etc etc etc
Bottom line is the guy made WAY more selling with Kindle/Amazon than with any other format, even given their large cut. That didn't just happen by magic. He is free to sell only with other vendors and make less money if Amazon's fees upset him so much.
No, it is indeed $3 to transmit a file. They even call it a "delivery fee". Consider that the percentage cut they take should cover all of the above.
I can get a physical pizza delivered for less than Amazon charges to send me an electronic file. That's just messed up.
Hell, I can get physical goods delivered, from Amazon, with 2 day shipping, for less than they charge to send an electronic file! And how much do you want to bet that the infrastructure involved in sending me physical goods is a lot more expensive and finicky than the infrastructure required to blast a file out over 3G?
No it is just a tiered pricing model. Either get 35% royalties and no delivery fee or get 70% and pay those very high fees. Almost all the things you include in the list apply to both pricing models.