As an individual, you are powerless when you go through the security line. As a group, however, the American people have all of the power. Because this is both a democracy and a capitalist country (however flawed it may be), if there is an organized and concerted effort against the TSA policies, they simply cannot stand. Congress would not be able to oppose a unified voice of the people saying "this is not okay" and the airlines would not be able to tolerate a significant reduction in customers (and therefore would put pressure on the TSA to change its policies).
Gandhi organized a "day of prayer and fasting" which was basically a general strike of all of India. It was a wake-up call to the British. If somebody organized a "do not fly" day where no one flew, that would probably be a bigger wake-up call than opting out of the scan.
Sometimes you have to give up some temporary convenience or comfort to send a message to those in power that you don't agree. During the Montgomery bus boycott, people stopped using the bus and this was extremely inconvenient but they would rather not trade their dignity for convenience.