As others have said, covers (in the pbook days, anyway) often grabbed my attention and caused me to be further interested in the book, which may have led to a sale. Presumably, bad covers caused those books to lose sales as I never investigated further.
One specific example of a bad cover interfering with sales involved the Colleen McCullough "Masters of Rome" series. Although these books are fairly substantial historical novels based on McCullough's reading of primary sources in Latin (with a lot of interesting and accurate political and historical detail, described in elaborate footnotes), the fact that the mass market paperbacks (in the early 90's, anyway) had cheesy covers that looked like they belonged on romance novels kept me from buying them for over a year. I had trouble reconciling what the book seemed to be about based on a quick glance at the contents as opposed to what the cover seemed to be suggesting that the book was about...so I didn't take the risk.
Here is an example of the MMPB cover style:
At some point her publishers must have realized what was going on, because later editions had a much more explicitly Classical look:
or
Note that this was probably 1992, where my usual method of looking for new books was to wander around the bookstore looking for books that caught my interest and then trying to determine whether I might like it by reading the cover blurb and some of the inside. How primitive we were then!
(As an aside, I always liked sf covers that depicted some scene from inside the book, since it was always cool when I reached that part of the book and realized *that's* what's on the cover.)