While a lot of times people complain about companies that still sell well, in this case I think Barnes & Noble's bad Web site is really hampering them. According to Mike Shatzkin, their 13.1% increase in e-book sales is far below what it should have been, despite being the company's best number by far. (I can see that--it's way below the 34% growth reported by traditional publishers, and of course if Barnes & Noble experienced 43% growth last year....)
Barnes & Noble Web store's design has been taken apart pretty thoroughly. But instead of focusing on improving the layout of its virtual store, Barnes & Noble followed the strategy of getting Nooks into other brick-and-mortar stores.
At this point, that's definitely looking like a critical mistake (and given how holiday sales went, I bet many of those retailers wished they had carried the Kindle instead). I also would say that it's symptomatic of Barnes & Noble's habit of simply not taking e-commerce seriously. This is a company that, back in the day, revolutionized book retail, but they don't seem to be willing to do even basic and obvious improvements to their online retail outlet (and of course they're busily pulling books out of their brick-and-mortar stores, therefore losing the expertise they had).
Passive Guy argues (convincingly, in my opinion) that the bad Web store pollutes the entire brand. Even if it just pollutes the e-book buying experience, that has serious ramifications: It takes ten seconds on Google to figure out that you could be reading Kindle books on your Nook, and one click more to realize there is an entire cottage industry dedicated to allowing Nook readers to NOT buy their books from Barnes & Noble.