"Let's not forget the process is basically owned by the TSA, and however the process goes it's their process and they're going to own the responsibility to make sure that process goes smoothly," said Hankoff.
Body scans take about 20 seconds but pat-downs take about two minutes. The TSA says if thousands of people do choose to opt out it could mean delays and missed connections for everyone.
"We're fully staffed. We can deal with every contingency we can but there is no guarantees that people get on that flight if there are a large number of people protesting," said John Pistole, the head administrator of the TSA.
The TSA's more stringent security measures are being called invasive by many. Other passengers are sympathetic but say they understand why the TSA has increased security.