Well, its always best to know the actual details of what was going on. The problem was that Amazon was selling its "e-books" (i.e. Kindle) versions of books for well below their cost they paid to the publishers to buy them. Several years into this Amazon also started its own publishing arm. In the end, assuming Amazon would demand low pricing like they were selling e-books for or not sell them (after all other large scale sellers had been eliminated) this would likely bankrupt and destroy much of the publishing industry (the industry and Apple could see this) - leaving Amazon with sales and much of the publishing to itself (a monopoly).
Apple talked with the publishers and said we want to sell e-books, but since they are electronic they need to be cheaper than the paper based versions, but the publishers have to make enough to be around (as nobody wants to just have Amazon destroy the publishing industry and be the only large scale publisher/seller of books in the U.S. - monopolies tend to not work out well for the consumer in the end).
So Apple was proposing lower prices for e-book versions, but the publishers would force Amazon to not sell their Kindle versions at a loss. This was illegal to coordinate & price fix like this, but it didn't raise the prices of e-books the publishers were selling, it lowered them (as they were selling them for the same price as paper versions to distributors, including Amazon, before hand - Amazon was just selling their e-books at large losses, presumably to destroy their competitors in the large scale book sales market & possibly with an eye to eventually corner the market in the publishing industry).