It's not $3 to transmit a file. It's $3 to:

Design a great UX

Handle Credit Cards safely

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.