Now, with the advent of Amazon, anyone can be a best seller based on very fine grained categories (as shown here) but claim the same accolades based on the title of Best Selling Author. A lot of people accept the title at face value. Over time, this shifts the power from the traditional lists to Amazon since Amazon has most of the power in determining who gets a "best seller" label and at what granularity.
I think this is what the author is really concerned about. In the article he mentions his job consists of working with authors to promote their books and their metric of success is aiming for the NYT best seller's list. If that list loses its value and the cache of being a NYT Best Selling Author decreases, then the author's value add to an individual author is diminished thereby threatening his underlying business model as it stands now.