Amazon is on pretty much every platform except the apple TV, so something is clearly wrong on Apple's end. Whatever the financials are, only Apple aren't offering Amazon acceptable terms.
Of course it's entirely counter productive for apple, as by keeping Amazon off the platform they make other, superior platforms look even better. Unless you own iTunes content, why would anyone buy any apple TV over a fire TV or a Roku?
The Apple TV is a flop, a total turkey. It offers nothing competing platforms or even smart TVs don't offer, and often much less.