I don't get that. It's just a deal. They could have said no. The rules of the game are clear. Amazon can make your app free unilaterally, but you'll still get 20%. Or, you go into any arbitrary mutual business agreement with them to guarantee that your app gets promoted, at the cost of lower/no revenue. I found the fact that the latter exists informative, but in no way threatening.
My take from this whole thing is that in the technology industry, people are not used to making business deals and get scared when they do.