The summary implies that the developers didn't know that they would get no money. The article makes it clear that they not only were told they would get nothing, but they confirmed in subsequent emails with Amazon that they would get nothing. Knowing this, they still decided to go ahead with the deal.
The Amazon emails have a good point:
The Free App of the Day promotion is the most valuable and visible spot in the store. It hosted the launch of the likes of Angry Birds Rio, Plants v. Zombies and more. Amazon will not receive any sales rev share from the Free App of the Day; and in fact, with as the Free of the Day for one day, you will receive a subsequent Appstore main page placement for the following 14 days. All these highly valuable placements are at no cost to you. We want to promote your app and in exchange of the placements, at the 0% rev share for one day only.
Being "Free app of the day" is a huge advert for your app - and adverts have a cost. Being app of the day is optional - not mandatory - the developers in question could have said no. And the cost is not 101,491 copies of your app - that's RIAA accounting. The majority of downloaders will try your app once and then never use it again. Some may continue to use it, and when they do, if you're smart you'll figure out a way to monetise their usage (e.g. charge for version 2, offer premium feature updates etc.).
thanks to Amazon's secret back-door deals, we made $0 on that day.
Amazon also made $0 that day (from your app). You agreed to the deal. It gave your app enormous exposure. You didn't lose 101,491 sales, because the vast majority of those people would never have bought your app anyway.
To the systems programmer, users and applications serve only to provide a test load.
