Given the choice between getting felt up through my clothes and having a naked picture taken, i'll take the feel up every time.
That, and I flatly do not trust these machines and who's administering them. It's a matter of when, not if someone (or lots of someones) gets a bad dose of radiation through these things.
It's a naked picture of you that doesn't really look anything like you and contains no identifying metadata. Imagine if the last 100 naked pictures from Logan ended up on the internet. Would anybody be able to identify them?
Maybe not, but they also have a list of exactly who was there at the time. We cannot examine the software, so we have no guarantee that it really blurs face and privates. Don't you think they might be able to do some analysis with either a full-body or partially blurred collection of scans over time?
It's not that it's different; it's a form of civil disobedience (which isn't even that disobedient) by requiring more time/energy/work on the part of the TSA agents. If enough people opt out, the line slows down, and the machine gets turned off.
appleflaxen put it well. Opting out is a method of showing TSA agents that some people think about these things and care. It also puts more demand on their limited time and resources. If everyone opted out they'd have to get rid of the procedure all together.
Aren't you still being searched by hand when you opt out, though? It that much different?