In 2013, Amazon had 65% market share of online book sales [1]. It wouldn't surprise me if this was 20% higher now.
When customers walk into a Barnes and Noble (or any bookstore) and browse books but don't buy (for example, because they found a cheaper price online), they are most likely to end up on Amazon to complete the purchase. B&N did the work but Amazon got the money.
Amazon doesn't have that problem. They don't need to sell books in the store to "pay the store's operating expense" - they just need people to come in and browse.
Currently, Amazon doesn't compete for a high percentage of books (50%) moved through physical stores [2]. They are in the enviable position of being able to create stores that don't leak sales to competitors. This is the final nail in B&N's coffin.
[1] http://www.thewire.com/business/2014/05/amazon-has-basically...
[2] http://www.dailydot.com/business/ebook-sales-2013-revenue/