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					Originally Posted by  wallcraft
					 
				 
				What may bother Amazon the most is the loss of the ability to discount ebooks, because large stores can do this more effectively than small stores. 
			
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 Exactly.  Amazon currently loses money on a bunch of their e-book sales; they're trying to push the Kindle.  By agreeing to Macmillan's terms, they're essentially being placed on equal footing with other e-book sellers (i.e., Apple...though will B&N, Kobo, etc. be subjected to this as well?), thus losing the advantage they have.
It's also worth reading 
Charles Stross's take on this.