For the record, my personal bugbear is the privacy implications of the new "advanced imaging" machines appearing at airports. But then again, I've distrusted supermarket loyalty cards and freeway FastLane programs, too -- my experience is that data which is collected will eventually escape your control (if you had any to begin with), and that no one is willing to offer a believable privacy pledge for such data (it would have to have 3rd-party audits for compliance, for example).
All that said, I just read a very reasonable article discussing the health impacts of the new scanners. I'm not going to play the alarmist card — ironically, the risks of injury from passing through a scanner are most likely about the risk of injury in a terrorism-related incident, that is to say extremely small — but it's prudent to admit honestly where risks are unknown, and to call the lie when deceptive arguments are used.
So let's not get all "ooh, scary, radiation" about this — quantum-physically speaking, everything is radiation at some wavelength — but it's worth keeping the risks in mind so you can make your own decisions, especially if you'd otherwise feel peer-pressured to "just do it". I'm just glad that as a nation we've apparently decided that this is where we're going to step up and draw the line, libertarians and liberals together. Contemplating our freedoms progessively and silently eroding away one by one is a far more worrying prospect.