This is an app, not a iBook. So this is a question about competing on the platform level.
If I’m Amazon, I don’t want to be in the hardware business. Amazon is a software company that builds a retail platform. If I’m Amazon, I want to write the Kindle app for the iPhone, iPad, Slate, Courier, etc. I want to sell books to people that use other people’s hardware. Amazon created the Kindle hardware because there wasn’t a suitable platform...at least for a certain segment of the market. The iPad has the potential to serve that same market, and Amazon stands to win by supporting the iPad.
It’s with the iBooks app and store that Apple is competing with Amazon.