It is news to me that this is not the way things work.
I mean really people, I hate to sound condescending, but... when you do a "buy one get one free" do you really think you got something for free?
Maybe one day we'll all get free healthcare and free schools and freeways too. Don't kid yourself, you're paying for them.
Remember the classic EBay scam back in the old days? You'd sell some widget for $5, with $25 shipping. Commissions were calculated on the item cost and excluded shipping.
Also, Amazon is making rule/practice changes that are eroding the benefit of Prime. In 2010, they would send products to me that weren't in east cost warehouses via 2nd Day air. These days, they usually just deliver it late.
Building shipping into the cost like Prime however, might do the reverse and expose a seller to over-refund issues where they would lose more on a refund if it must include the total item price without shipping. (When shipping is "free" and built in to the item price.)
To reiterate the parent comment: No, but we are paying a non-trivial fee for Prime membership every year. Is it unreasonable to have thought that part of that fee would go to offsetting shipping fees to the original seller?
I found your post informative in that, no, in fact it does not. That was definitely news to me. But no need to be condescending about it.