In addition to all the (basically lazy) reasons to buy Baen eBooks from Amazon, there is actually one very good reason to do so -- WhisperSync for Voice, and the deals that come with it. For many Baen books, this means the Audible book is very cheap - ~$2.99 or less. But more importantly, the eBook and Audio Book work together, allowing you to go back and forth without losing your place. Or, if you have a Kindle Fire, you can do "total immersion" reading, with the audio book being read out loud as you read the eBook.
That being said, I still prefer to get my Baen books from Baen, in the hope and expectation that the authors actually get more of the proceeds, though I don't actually know that for fact. But I have resorted to buying a few from Amazon to enable a really good deal on the Audible book.