Justine Larbalestier points to all the things an author has no control over, which is useful information for when, say, you look at a book cover and wonder to yourself what the hell the author was thinking. Justine’s list is pretty much correct (there are a couple other additions to the list in the comment threads), although I would make the caveat that some of this is contingent on other factors. There are some of my books which I have had quite a lot of participation on things like cover and jacket copy and so on — but in all of those cases that was contingent on the willingness of the publisher/editor to let me be involved. The point is ultimately the decisions on a lot of things about the books is not the author’s.
It’s also worth noting that this is not always a bad thing. A writer’s core competency is writing, it’s not book design or art or marketing… or how all three of those fit together, for example, to sell a book. Writing a novel is largely a personal endeavor, but turning that novel into a book is a group endeavor, as is selling it. When you’re lucky, the other people you’re working with are good at what they do, and you can trust them to do their jobs well — so you can focus on writing.