If you actually want to get value from a security measure you need to ensure that people can't just bypass it. Consider the case of a terrorist carrying some device which won't show up on the magnetometer but will show up on the whole body imager; you just choose the line with the magnetometer.
Now, most likely the TSA is just getting started up here and eventually they will actually have scanners in every line and make everyone use them. After all, presumably they're not planning to have a bunch of scanners whose only purpose is be something for TSA screeners to lean against. What I'm curious about is whether at SFO TSA will give you the enhanced pat down if you refuse the body scan, since you could have evaded it easily without coming to their attention just by picking the right line.