See Reddit clients vs charging for API debate
If apple wants to shut down beeper, there is a very very very easy way. Release iMessage for android. And suddenly beeper is dead overnight. All they have to do is build the product people want.
Beeper's problem isn't implementing the iMessage API but providing access to Apple's infrastructure without authorization.
The answer seems to be Apple wants to force families to purchase an iPhone for every family member, or download and agree to the terms of a third-party app in order to securely communicate.
The difference is that Apple's business model is built around preventing you from communicating with iMessage while Amazon is happy to let you copy things from anywhere into or out of your Amazon S3 bucket (for a price.)