The source of the confusion here is obvious and pounding on it won't help. From the DoJ's perspective Tor is hidden services. Criminal abuse enabled by proxying to the open web is not high up on their radar. Regular web sites can easily block Tor. But hidden services are unique. When Tor is mentioned in the media, it's almost always because of hidden services. When it's involved in large scale FBI investigations, it's almost always because of hidden services.

So whilst Andy Greenberg's article is correct, it's correct in a nitpicky technical sense that isn't going to have any political impact as an argument. Tor has chosen to support hidden services very strongly, so the fact that it's a relatively small amount of their total traffic doesn't matter much.

The Tor project needs to take this kind of thing seriously. Alarm bells should be ringing. They are getting (apparently credible?) tipoffs about plans to seize directory authorities. Relays actually are getting seized. DoJ officials are publicly saying they perceive Tor as being dominated by crime. Meanwhile they are doubling down and making blog posts that describe police operations as "attacks". This has the feeling of a slow motion train wreck in the making.