Two key points of difference:
1. Genre-based marketing. With a paper book, the cover design, artwork, pull quotes, title, and other front material—and the publisher's imprint logo—serve to tell the bookstore staff which shelves to put the item on, and to cue readers that this book is similar to others with similar design values. That's all. Genre is basically just a tag to identify how the item is to be sold.
Because this system is static, printed on paper and card, it's inflexible. You can't easily market a novel as both crime fiction and SF simultaneously; you have to pick one, or the other, and hope to hell that the genre you put the product in is the one that will sell best.
You can, in principle, put different covers on the same book. But it's expensive, and you also have to get the [reluctant] distribution channel, the booksellers, to understand why you're trying to jam twice as much content down their throats to fill their precious shelf-inches. (After all, they can't sell something if they don't have shelf space to display it on.) It works for bestsellers like the early Harry Potter books while they were breaking. For midlist authors? Go away!
Ebooks don't need to take this one-shot approach to marketing. It's possible to apply multiple genre tags to books; Amazon already do this. With a bit better storefront design it's possible to give readers browsing by genre views of titles that they otherwise wouldn't notice. It's even possible (in principle) to design different covers to display to readers using different search criteria. Expensive, but possible.
2. No reprint delays. If a hardcover breaks big in its first week on the bookshelves, it will rapidly sell out and be replaced by ... empty shelves! Yes, publishers can go back to press. And they do. And in this age of PDF-to-press printing, it's possible to have more hardbacks available within a matter of several days to a couple of weeks. (The same goes for paperbacks.) But in the meantime, the ramp-up in sales, and thereby the ramp-up in reader interest, stalls and goes off the boil.
With ebooks every print run is infinite. I suspect this is behind the success of titles such as "Fifty Shades of Grey". Ignoring its explosive bestseller growth in print for a moment, FSoG started out as a purely ebook phenomenon. If it had been printed the traditional way, in a run of 2000-8000 hardbacks, they'd have sold out. Period. A few weeks later a trickle of new stock would have shown up in the bookstores. Meanwhile, everyone would have forgotten the title of that sizzler they'd been reading a couple of weeks ago, thereby depriving their friends of the hot tip.
Other key points:
What other fundamental differences can you think of, from a publisher's viewpoint? (Not including the whole DRM/file format stuff we routinely rehash here. I'm looking for angles that change the shape of the whole game.)