The amount of radiation that body scanner supposedly put'* out is supposedly less than background radiation we encounter daily, medical procedures, etc. My issue with them is that they still do not know the long term affects for this type of highly concentrated millimeter x-ray beam - in conjunction with all the other bombardments we face daily.
There have been studies and mathematical models done that indicate that these devices are not as safe as lead to believe. Couple of good resources are http://en.wikipedia.org/wiki/Millimeter_wave_scanner
I'm all for safety measures that improve our safety in our lives as long as it'* not intrusive and my rights under the fourth amendment are not compromised:
...... The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.
In my opinion...the scanners and pat downs are unreasonable. But...that'* just my opinion and I'm sure will face legal challenges in the years to come.