If you go with the argument that Apple is a hardware company versus a software or an apps company then I can see them allowing all of the reader apps. And if you look at Apple's sales figures, the hardware far outsells the software and the apps.
Check out this figure:
As you can see Apple makes most of their revenue from hardware sales so it would make sense for them to allow as many apps as possible in order to sell more hardware.
I wonder how much pull the publishers have in this?