Buried in the article is information from Amazon that ebook sales are continuing to rise. But this article isn't about ebook sales -- it's about big publisher ebook sales.
The article also says that dedicated ebook reader sales have declined. This is true but not because of a shift away from ebooks. It's that ebook reading is shifting to tablets and phones, a trend that is widely recognized in the industry, but not in this article.
The reason that big publishers (and some smaller publishers following the traditional model) are losing ebook sales is that, in the big Hachette - Amazon dustup last year, the big publishers won the ability to keep ebook prices ridiculously high and to prevent discounting by Amazon. So big publishers routinely price ebooks about the same or higher than paperbacks. Of course their ebook sales are suffering! But self-pubbed and indie publisher books are priced much lower than print books, and are of course gaining market share very quickly.
The NY Times reports on publishing are all biased toward big traditional publishers - after all, that's essentially what the Times is. (To the Times' credit, they have a public editor who critiques their stories, and the public editor has said that the last two major stories in the Times about Amazon failed to meet journalistic standards.) They ignore information like what's on authorearnings.com because they're trying to get people to believe there's a trend away from ebooks. There certainly are some people who decide what kind of book to buy according to what they think the latest trend is. But if you're looking for accurate information about the book business, don't expect it from the Times.