You are not missing something the author has obviously mixed up the "dark web" and tor.
>TOR, short for The Onion Router, is an obscure routing network that allows anonymous access to the “darknet” — the vast, murky portion of the Internet that cannot be indexed by standard search engines.
>Estimated to be 5,000 times larger that the “surface” web, it’s in these recesses that you’ll find human-trafficking rings, black market drug markets and terrorist networks.
[edit: To be perfectly clear, I was only highlighting what was actually said. I don't know anything about the dark webs.]
http://en.wikipedia.org/wiki/Dark_Internet
http://en.wikipedia.org/wiki/Tor_(anonymity_network)
These are three completely different things.
I guess the way it's written it's technically true - if you count the darknet as part of the deepweb, then it is indeed in the deepweb that you find the nasty bits. But that's extremely disingenuous, and it seems more likely that the author doesn't understand it.