I've been doing quite a bit of traveling lately, and every time when confronted with one of these machines, I've chosen the alternative pat-down (it's your right, you can request this). Why? I simply don't trust them for the radiation exposure despite the claims that they are safe. I have NEVER seen them allow an infant through these systems--they just wave the mother/father around the device with the infant in their arms (and with no alternative pat-down for the parent...). If the TSA will not allow infants through the system, obviously they don't think the exposure levels are completely safe.
So anyway, sure, the alternative pat-down is super-invasive, but at least you avoid accumulated exposure. I only travel 5-6 time/year max., but for folks that might travel several times per month, I can imagine the accumulated exposure over many years will not be completely benign.
A side effect of requesting an alternative pat-down is that it seems to throw the system into convulsions. They start radio'ing around about needing somebody to deal with the "refuser", and waiting for someone to arrive can be either fast/immediate or slow (like 5+ minutes). For being a "refuser", besides the pat-down, you seem to obligatorily get swabbed/analyzed for explosive residue.
All in all, if just one person every few minutes were to request such an alternative pat-down, it would overwhelm the system. The problem with this is that they then just start waving people through to avoid clogging the pipes. So these people get a metal detector only--not a pat-down nor the full-body scan. If they just let people through like this, well, what is the whole purpose of this anyways???