Because when B&N's Nook came out, nobody talked about changing e-book prices. They sold at $9.99 everywhere, mostly because that's what Amazon said e-books should sell at. Publishers got the same cut they always do with this pricing, and Amazon took a bigger loss than on print books. But Amazon liked this pricing because it's a loss leader for them to sell Kindles.
Macmillan (along with other publishers) was concerned that $9.99 was unsustainable in the long run, yet would become the "normal" price for e-books if unchecked. They wanted a deal where publishers chose e-book prices (usually in a range from $5.99-$14.99), and the sellers (Amazon, Apple, etc.) got a larger cut. Apple said, "Sure." Amazon said, "No way," and just to show Macmillan who was boss, Amazon pulled the Buy buttons off of all Macmillan products, digital and print. That was 1.5 months ago.
Amazon eventually caved and said they would put the Buy buttons back (which they did, but very slowly; I'm not even sure they've put them all back yet). But now a bunch of other major publishers are saying they want the same deal, and Amazon is threatening to pull the Buy buttons on them.
Really, this is a struggle between Amazon and publishers. Apple is just a battlefield, chosen because the iPad is the only e-reader that can strongly compete with the Kindle. If publishers tried to do this fight with the Nook, Amazon would've just laughed at them.
