It's called "delivery fee", not "delivery cost". It makes no sense to require a business to charge fees solely based on variable costs.
So many commenters seem to see the $2.58 as Amazon saying "this is what it really costs us". I'd think it means something more like "this is punitively high so please make your book smaller."
I disagree with both sentiments.
Main point: It does not cost amazon an average of $2.58 to deliver the author's pdf. Amazon is being dishonest by calling this a delivery cost. I consider it unethical to name a fee something that it is not.
"Be grateful for what you do get" is not a valid argument against dishonesty. If Amazon makes a business decision to take a loss on kindles, this also does not justify dishonesty.