The fact that once you purchase a plane ticket, you're submitting to all rules and regulations associated with air travel leaves you only two choices. Fly and put up with it, or find alternate modes of travel.
Yes you can protest and shake your fists at the corporate interests (the only reason why the machines and subsequently the enhanced pat downs are there, not security) of former DHS head Chertoff. I really don't think they are going to care.
For me, I'll still fly and choose getting my nuts juggled a bit vs. cancer... but when traveling with my kids, I will probably take a train or drive depending on distance. For however long those options are available without being radiated or felt up.