There's been information in their shareholder reports about how the average Amazon Prime user spends $500 more a year on various items on Amazon.com than a non-Amazon Prime user. I believe that statistic is from 2013. There are 79 million Amazon Prime users. So Amazon's revenue for THAT program is $99 + $500 for each of those users.
Amazon uses the Prime program to promote their own imprint books (kindle first program), to draw traffic to the site. All of us here talk about our permafree books and 99 books as being loss leaders, well, to Amazon, WE are the loss leaders.

Ebooks, with their little to no overhead costs, are nearly pure profit for Amazon. Then, when you start leveraging those nearly pure profit products to bring people into your store EVEN more, you're really winning.
I am a KU user, but not a KU author. I have spent additional monies every single month in the program above my $9.99 because I discovered a book I wanted to read that wasn't in KU and was an Also Bought, especially on some non-fiction titles. Yesterday, I read the 9 Days Novel book, a KU title, then I bought James Scott Bell's Writing from the Middle because Amazon showed me that title (I'm a huge James Scott Bell writing book fan) and I didn't have that title. I almost passed because of the cover, but that's another story entirely. Anyway, Amazon got $3 in revenue from me they wouldn't have if I hadn't been in the store to grab 9 Day Novel book. They make at least $1 on that purchase.
It's like super stores that run specials on things people need all the time, if I can get you to come to MY grocery store for milk because my milk is $1 cheaper than the other grocery store in town, chances are you aren't ONLY buying that milk, you'll buy other stuff. Amazon has to keep us coming into the store more often, because if we're not on the site, not on our Kindles, not reading in the app, we aren't buying more books.