As someone walking all sides of the fence (graphic designer by education & trade, writer by night, and designer of book covers for a small publishing company)..... It's a tangled web.
I think it all comes down to the designer, but the designer is dependent on the imprint & the author input - it's hard to make something great if all you get to work with is crap. Not impossible, but hard.
If you have an imprint that is cheap, then getting the resources to make a good cover is hard (time which they typically are paying for by the hour, photo or illustration resources). Given the opportunity to use all the resources effectively it would be impossible for any graphic designer worth their weight to make a bad cover.
If the imprint (or the author, depending on how involved they are in the process) that restricts and micromanages every thing it's hard to get quality anything. Check out this comic--->
http://theoatmeal.com/comics/design_hell
And sometimes there's the case where the imprint/author fails to provide any direction whatsoever on the book... in which case the designer is shooting in the dark with the only thing to go on is the book's title and a guesstimate on what it's about.
ANNNNND then we have the sad case of where everything in the book cover creation environment is perfect for book cover awesomeness... and the designer behind the wheel sucks.
To wrap up my long-winded reply, what makes a quality book cover?
Everything going right