Microsoft Windows is pretty expensive for an OS...its main competitors are literally free. But since they aren't a near-perfect replacement for Windows, Microsoft can charge more per unit. This is pretty similar to how LCDs are not a near-perfect replacement for eInk displays and that there's essentially only 1 mature supplier they can charge more per unit than an LCD manufacturer can.
Since again, the display tech is essentially what defines a Kindle Amazon is somewhat forced to use eInk displays despite their higher cost otherwise it would not be the same product.