This article seems seriously confused about how Tor works ("only the ISP used along with it can ascertain what activity takes place on Tor"), such that I don't trust the rest of what it's saying. There is probably no story here.
http://www.netresec.com/?page=Blog&month=2013-04&post=Detect...
Not even this much, actually. Tor doesn't do any sort of protection on the traffic; it just routes it cleverly. The packets themselves are still plaintext if you're not using an encrypted protocol (e.g. HTTPS) on top of Tor.
In practice, most people use Tor through the browser bundle, which includes an HTTPS-Only extension. But if you're routing random other protocols through Tor (e.g. XMPP, BitTorrent, etc.) be aware that Tor is not doing any protection of your plaintext; that's the responsibility of your client/protocol.
I helped make this diagram to demonstrate these details:
Tor encrypts your traffic within the Tor network. Even if you don't encrypt, Tor does automatically so your ISP cannot see your content.
If you don't encrypt, your content will be visible to the exit node, but not to your ISP.
To be fair, this is a dumb error and I wish they would issue an honest correction rather than simply removing the incorrect part.
Since then, it does appear that phrase has been redacted. It would be nice if they published a correction, though.
But this entire article seems to be based off random complaints by people on reddit. There is nothing to go on here.