"Each full body scan of the Secure 1000 produces approximately 3 microREMs of emission. This is equivalent to the exposure every person receives each five minutes from naturally occurring background environmental radioactivity"

Average exposure in daily life is 300 millirems per year, or 300,000 microrems, so their math would appear to be correct.

FYI, The airplane ride itself is 500 microrems/hour at cruise altitude.

The harm is pretty much limited to civil liberties.