Yes, their motivation is understandable. However it's pretty unprecedented for the creator of a software platform to get a cut of all transactions that take place on that platform.
Apple doesn't expect 30% of Kindle books sold through the Kindle app for OSX. I really don't see why there's such a difference. OSX and iOS are made by the same company, and both run on only proprietary hardware. I'm not sure why iOS being an OS for phones and tablets means Apple is reasonable to expect 30% of all transactions.
The real issue here is that Apple controls what apps can and can't run on iOS. They can't tell Amazon not to make Kindle for OSX, because users can install whatever apps they want on OSX without the App Store. They can ban apps from the Mac App Store, but that's it.
Without Apple's monopoly on iOS app distribution, they couldn't get away with this. Had they stuck with their original plan of taking 30% regardless of whether there was a link to the store, Kindle, Hulu, etc. would have pulled their apps from the store and distributed them via their web site - if they were *able* to distribute apps themselves.
There's a flawed idea out there that developers owe Apple for giving them this great platform to work on. In reality, it's a two-way street. Developers need a platform, a platform needs developers. iOS wouldn't be nearly as popular without third-party apps. It's not just mobile platforms - can you imagine Windows or OSX without third-party software?