I'll give you that judging like that may be more problematic on science fiction than fantasy novels, and that more Sci-Fi novels might have crap covers, but I'm mainly a fantasy reader, so I couldn't say more on Sci-Fi books specifically. That said I'd disagree with you on the fact that the vast majority of (at least fantasy) good novels have absolute shit covers. Something like the Mistborn books might not have the best cover:
But it certainly passes the "this book looks like crap" point enough that I'd check the back/inside cover for a more in-depth look. Other books can go well beyond that mark, and plunge well into the "high quality" range IMO. For example the books in the Broken Empire Trilogy are definitely high quality covers without necessarily being busy ones, and they rate as one of my more enjoyed trilogies.
On the other hand I'd say that of those books that I've read I'd definitely say that my most enjoyed fantasy books come mainly from those with higher quality covers, while I've yet to have a fantasy book with a cover that falls below the "this book looks like crap" mark that has made it anywhere close to my "favorites" list, most falling strongly into the "worth it only because the book was $1" area.
A lot of Discworld books have fairly cheesy cover art (in some versions) for instance.
I'd agree with that, and they're one of the few series with cheesier art that I've enjoyed. That said it certainly wasn't the cheesy covered ones that drew me into the series, but the more simple ones like The Color of Magic.
Once again I'll reiterate that the point isn't to solely judge a book by it's cover, it's to simply aid me in quickly separating the crap 90% out of the mix. Most of my book buying is done in large chunks when my family stops by while on a trip or something similar. When you only have some 1-2 hours to get through 80 feet worth of shelves (that's floor distance, not counting multiple shelves) that look like this
in order to take advantage of your parent's sweet 10% teacher discount, you have to be able to quickly sort books into the "not worth looking at" and "worth more time to see if it's good" piles.