Sure, your profit margin may be higher if a reader buys directly from your site. But you'll probably lose more sales to people who just aren't comfortable buying from a stranger, or prefer buying at a retailer where they already have an account or perhaps can combine their shipments.
Selection is important to book buyers, so the best strategy for authors and publishers is to be visible everywhere and available through every possible retail channel. "You need to be channel-agnostic," says Bill Schubart, president of Resolution Inc., a consulting firm. "All of the power has moved from you, the publisher, to your customer, the readers. They will buy the book how, when and where they want. Your job is to make it easy and intuitive."