This is like saying Henry Ford designed the modern automobile to be used in bank robberies, drunk driving murders, hit-and-run maimings, and kidnapping.
Yes, virtual currency is attractive to criminals. It's also attractive to law-abiding citizens, many of whom do not like to be lumped into one big morass with "organized crime" stuck on top as a label. We're stepping dangerously close to "If criminals like doing it, it must be bad" reasoning.
ADD: I also note this section: "...On Tuesday, in the first use of the 2001 Patriot Act against a virtual currency, the Treasury Department invoked a section of the law to choke off Liberty Reserve from the U.S. financial system..."
Well, there's your terrorism act, used to control crime via virtual currency. We get scared of one thing, pass a law, and then see it used in a completely different context. The current American kerfuffle involving investigating reporters is tied to a WWI-era law that's almost never used. Amazing the tools American prosecutors have available to them. One could say overbearing, even.
ADD2: Nobody is saying they are innocent. The point here is that these guys are being shut down (and they probably need to be shut down) by procedures that have broad application to all kinds of legitimate use as well. These are very broad and powerful tools we've given the state. We should take some time and think about if they need to be more narrowly-focused. The initial Patriot Act had an expiration date. For a reason.