A FOSS Operating System such as ubuntu needs $$ to maintain its quality, like it or not. You can download it for free, and you can even play around with the source code. You get what you pay for.
Plus, if enough revenue comes in through ubuntu, Amazon will take note and if future commercial relations happen between them, that could only mean a rise in ubuntu's (and by extension linux/gnu/FOSS) popularity.
Ubuntu-powered ebook readers anyone?