"Readers continue to leave print newspapers, but they’re not migrating to the online editions."
Because they have more options.
Print products were often monopolies, especially in the early to mid 90s, a hey day for newspapers. There was often a single publication per DMA.
What happened then is newspaper readers increasingly became web users throughout the 90s and 00s and left the print product. In 2000, if you wanted semi-local or regional news on the web, you went to ... your newspaper web site! In 2016, you have a plethora of choices, many of them unsaddled by the constraints of a typical newspaper organizational structure (for better or worse). So you have web sites and publications producing/sharing/clickbaiting 10x the content than your local newspaper does. This leads to a spreading of readership.
What's happened is a diaspora. Sticking with the print product over the web would not have prevented this. It may have slowed the decline of print circulation, but I have serious doubts about that. The challenge newspapers have is competing with decidedly non-journalistic approaches to news; ones that give readers what they want even if it isn't done "right." Competing with platforms and sites that can churn out "content" at an unfettered rate means fundamentally changing what a newspaper does.
There's no easy answer - newspapers can accept that people will largely go to other sites to get less reliable information faster, or that their content will be repurposed on other platforms without any compensation. That will likely mean a slow constriction or demise. Alternately, they can compete in that space, which a lot are doing now. That means sacrificing the ideals of journalism.