Security Flaw Shows Tor Anonymity Network Dominated By Botnet Traffic

This doesn't seem to me to mean as much as the author thinks.

By the same reasoning, after all, email as a communication mechanism is "dominated by" spam, much of it similarly shady in nature.

There is an interesting difference, though -- while spam actively hurts the usability of email, botnet traffic which parasites on the TOR network helps make the system as a whole stronger, by adding more noise in which the important uses of TOR can be lost.