Why did Amazon pull 5000 ebooks off the shelves?

There's been some fuss about Amazon pulling 5000 titles. In fact, the Gizmodo article barely explains anything beyond that, noting in two terse and profoundly unilluminating sentences:

Almost 5,000 eBooks have been pulled from the the Kindle Store because of a change made to Independent Publishers Group's contract with the online seller. The move is a result of Amazon's demand for upfront payment from publishers, required to host their books on the store.

But what is really behind this? Amazon is eliminating intermediaries. IPG represents many small publishers. Amazon, apparently, would rather work directly with these publishers, or even with the authors themselves.