Well, that's what the Tor Project claims. It's good marketing, but they're essentially lying by omission here.
But so is the "clear Internet", really. Sure there is a high proportion of innocent traffic, but if you think in terms of criminal activities, I am sure it is non-negligible. From copyright infringement to child pornography to revenge porn to harassment to unlawful handling of data. I have no numbers to back it up, but I'm quite sure a lot of crimes are committed on the "clear net".
And yet, it would be very unreasonable to shut the Internet down over this. Punish the person and their actions, not their tools.