First, the company is still heavily dependent on its brick and mortar retail operations, but the demand for physical media (including books) is declining rapidly. Second, the company's future depends on its ability to transform itself into a digital distributor of content. In digital distribution, B&N must contend with Amazon, Apple, Google, and others (e.g., Sony). These competitors have significant advantages in the areas of economies scale and scope and technology.
Borders bankruptcy will give B&N some reprieve, allowing the company to direct cash flow from its bricks & mortar operations to its developing digital strategy (e.g., BN.com, Nook). Nevertheless, I think B&N will face a rocky future. Investors seem to agree, with B&N trading at close to a 5-year low.