From the article:
"But he insisted that, by highlighting the unresolved problem, Google Flu Trends made things worse. “I think this does change the game,” he said. “Google is inviting public health officials to make more of search information. In doing so, it has heightened the privacy risk to people who search for health information online.”

Or perhaps it has just let people know that if they are concerned about the privacy of those searches, they should use a computer at their local library or some other place where tracking them would be harder."

Maybe, it is our notion of privacy that is ought to change? after all whenever we use a new technology it bounds to use the user as well..

This is why I don't use Google at all, and run TrackMeNot on my Firefox.