Good question; I wondered the same thing the first time that I saw the linked press release.

Their FAQ says:

At this time, evaluating the effectiveness of a charity's programs is out of our scope. We hope over time to expand the information we provide donors, and that includes developing a methodology for measuring an organization's output. For now we're still seeking a methodology that would allow us to apply a uniform standard to all charities and thus allow us to continue to provide donors unbiased, trustworthy ratings.

According to a recent blog post at Tactical Philanthropy, they're planning on adopting new rating system.