For those unfamiliar with the situation, the Flame malware propagates by doing a man-in-the-middle attack using a vulnerability in Windows which causes it to believe that a phony CA Cert was actually signed by Microsoft.

The last line of the article is the best one (emphasis and italics added):

I guess the good news is that this wasn't done by cyber criminals interested in financial benefit. They could have infected millions of computers. Instead, this technique has been used in targeted attacks, most likely launched by a Western intelligence agency.

Not to name any names, but Western intelligence is increasingly hard to find.