The non-fiction market depends on the kind of non-fiction. Highly researched, academic writing of course takes a huge amount of time not only to create, but, often, to publish. From the time the first full “draft” of the book is turned in (and by “draft” I mean something that has already been edited by the press, etc., so that’s about year to two from proposal to that stage, esp. if it is a collection), until it is actually in your hands can be well over a year. If by “non-fiction” you mean essays that people write, like on Medium, the time of composition is a lot shorter. I’m never going to make anything of my academic work, except, as you note, reputation, which might lead to more lucrative positions, etc. (I’m an English Prof, and I study the Middle Ages, to give you an idea of how little I make.)
But yes, another big cost that is often ignored is time. How much it takes to create something, to research it, etc.
Though I will say, that $1000 for a cover is a bit much, same for formatting, if you’re doing it yourself. I know people who will format a book (granted, it is usually fiction) for ebook, etc. for $100 or less, depending. So, you can do a cover and formatting for $500 easy if you know where to look. Of course, figuring out where it look takes (wait for it!) TIME. :)