In a retail environment, the choice of product position on a shelf or display is often not entirely the random choice of the retailer; the producer may be paying for that. IN publishing, where I work, there's a system known as 'coop' (cooperative marketing) in which the publisher credits the bookseller in exchange for favorable positions on a table or other visible spot (it's legal as long as the deal is clear to all and terms are offered to all). Normally these sorts of promotional considerations are hidden from the consumer. Recall that back when Amazon was still primarily a bookseller, they had actual category editors who chose books to be featured on the category's opening page.

So just having paid advertising is just an extension of this. As Amazon acts less like a department store and more like the operator of a bazaar with thousands of merchants hawking their wares in the street, I guess it makes sense.