The reason I like shopping and buying books there is the sheer selection. Of course, their footprint is much larger than BN. But BN could raise funds to expand their stores slowly and see if it works. Powell's has several floors of books and are probably larger than many large libraries in big cities. Next to each new book they also stock used books of similar or the same titles.
I just really enjoy the act of flipping through an entire book and then buying it on the spot. I don't think paging through the ToC in PDF form a la Amazon is that nice and I hate waiting for shipping. Plus, if on a technical book I'm going to spend $100 then I need to make sure for myself it's a decent reference.
It's been painful to see BN push the Nook. And to see them try to be a coffee shop. And CD store. etc etc. For the size of their store, they have a remarkably small selection of books, and they're all high-priced... and they complain they can't sell many books. Sorry, when I walk in to the store and see 4 crappy books on CSS, 10 on HTML, 5 on Windows, and a smattering of others, I'm not that inspired. But in Powell's technical bookstore, when there's a whole aisle on Javascript, I get excited.