First, from the consumer's point of view, they expect to pay once and not have to buy individual formats. So consumers don't exactly like paying twice for the same thing.
Actually though, even though publishers often have to charge twice for the same product in a different format, in some cases the second format provides an additional benefit for consumers, and also sometimes formatting it into a second format can cost a bit.
This is not as much of an issue now as it used to be, but up until about 2013, the effort to format an ebook for Kindle was probably 3x as much as the effort required to produce an epub format. Until Kindle released the KF8 format, the .mobi format was buggy, incomprehensible and a major time suck. Amazon was spectacular at marketing the Kindle, but they hadn't bothered to use an internationally accepted standard and so publishers had to go through all kinds of hoops to make things look minimally adequate.
Since that time ebooks formatted for Kindle are a lot better and easier to produce and test. Personally, my ebook publishing company which I run still spends about 50% more time formatting and testing for Kindle than for epubs, but at some point you develop one template that works, and as long as the formatting is not too complex, the extra costs diminish over time.
You would think that producing a print book and a pdf would not require much extra effort. But Amazon doesn't sell PDFs, and the workflow for both formats can be different. So there is extra effort involved.
My answer then would be that the publisher states a price that reflects the market value and compensates the publisher for production efforts. I've seen some companies sell a bundle of ebook + print for slightly extra and other publishers who sell them as two separate products. There is no right answer here. My point is to say that sometimes producing something in an extra format costs the publisher/writer extra money.
At the moment, I am re-formatting an ebook published in 2010 which looked perfectly good in Kindles up until 2012 or so, but after Amazon changed to KF8, started to look like crap. From a financial perspective, this extra effort doesn't justify the payoff. A publisher shouldn't have to reformat an ebook just to make it minimally presentable. But in 2010-2011, most of the ebooks formatted then looked terrible on Kindles. This can exact a toll on publishers unwilling to retrofit the ebook to newer standards. At some point it has to do with commitment to quality. But look at the music recording industry. Often labels will re-sell the same album which is re-mastered to contemporary standards. Nobody would expect that the label should give it to free to people who purchased a previous version of it. But with cloud based products or services, customers have different expectations.
By the way, smashwords.com has a work process which involves BUY ONCE, download in multiple formats. The only catch is that you have to submit using Smashwords own production methods.