Exactly. Loss leader, plus the fact that they now have a list of customers that are not only active and recurring but quite literally pay Amazon to buy from them. The avg yearly purchases of an Amazon Prime member is more than double the site avg.
I also think there's a sense of membership that if you are paying you might as well enjoy the benefits.
I personally enjoy Amazons packaging. I know my items will be well packaged, whereas there's always a surprise on Ebay or other store. I have chosen ship with Prime (Fulfilled by Amazon) on items that other Amazon sellers have cheaper.
It's just more consistent and efficient. And that's sort of a benefit.