A particularly telling comment from one of the editor/art directors was that buyers for chains have enormous power. If they hate a cover, the publisher will sometimes re-do it, because if they don't want to buy a book with that cover then that book has little chance of selling well. This includes not only Borders and Barnes and Noble buyers but big box stores like Walmart.
But more specifically, the reason I started this post, was that Lou Anders of Pyr commented on the book Infoquake by David Louis Edelman. He called Edelman a genius, and said that because Pyr thought the book could appeal to mainstream audiences, they put a mainstream sort of cover on it; it's not obvious the sphere is a planet(Correction from the author: DLE says the sphere is in fact, a building). However, when it hit the stores, the book was shelved in science fiction. Anders' contention was that the science fiction audience was less than impressed with the rather abstract cover. Thus, the next book in the series has a much more science fictional cover with a futuristic cityscape.
And yet, a recent item on GalleyCat waxes enthusiastic on some Gollancz (UK) covers that don't look typically spec fic—even more abstract than Infoquake, in fact. Hmm. Maybe they should have called Lou Anders first?