Needless to say, the Internet has harmed--if not destroyed--the market for specific kinds of nonfiction books. To cite an obvious example: It wouldn't be a great time to start a publishing firm that specializes in atlases, given the competition from Google Maps.
But what the Internet will ultimately chip away at will be the superficial and the commoditized. An atlas, even in the days of print-only, was nothing more than a tool.
The Internet is unlikely to replace deeper, more immersive reading experiences that involve extensive explanation and analysis. And that has always been where the big money is in nonfiction publishing.