There is nothing wrong with Apple's way. Amazon's way undermines the capitalist system. Also, they (Amazon) still sold the books at a fixed price in order to undermine competitors and may have been forcing publishers and others down the line to take a loss on each book sold. That is wrong. The government is wrong in this case.
I am not saying either side is right or wrong. Both Amazon and Apple are trying to maximize their present and future ebook profits by molding the market to their whims.
That being said, I sure don't see how Amazon is "undermining the capitalist system". The publisher gets 50% of the retail cost per book sold. If the publisher wants to make more money they can increase the retail cost. If they want to increase sales they can lower the price. Of course if they increase it too much nobody will be buying the book. That sounds like capitalism at its' finest. Also the publisher is free to ask for more than 50% if they so choose.
What you don't seem to understand is that when Amazon is selling the books at a loss, it is
Amazon's loss, not that of the author or the publisher. The publisher still gets 50% of retail for each book sold no matter what Amazon is selling the book for. Amazon is willing to take that loss in order to increase market share. Sucks for everybody else out there for sure but that is what is being done. Amazon is not forcing publishers into a fixed price, Amazon is setting their own price
after they have purchased each copy of the book from the publisher.
The government is only wrong in this case if there is no collusion amongst Apple and/or the major publishers in fixing the prices of ebooks. Price fixing in such a case violates US law and is under the perview of the government.