In a USA Today opinion piece, Napolitano claimed that body scanners and pat-downs were for safety purposes and other measures were in place to protect travelers' privacy.
Over the weekend, a man refused to go through a full body scanner at Lindberg Field Airport in San Diego, calling the security measure excessive.
"They asked me to go through the scanner, I told them, 'I don't think so.' I think those are literally the words I used," said 31-year-old John Tyner of San Diego. "We're spending inordinate amounts of money on security that isn't necessary and arguably doesn't work. I didn't intend to go through the machine or be groped."
After talking to airport officials, Tyner was escorted out of the airport. He got a refund on his ticket but could face legal charges for not finishing the security screening process.
Some travelers at Los Angeles International Airport on Monday said they new procedure wasn't so bad.
"They were pretty respectful about it," said Lina Bird of West Virginia. "They searched through my bag, patted down my legs and arms, my front and back. They were polite, so I really didn't mind."
"Consequently, I think we're all safer if we subject ourselves to that sometimes," said another traveler passing through LAX, Roy Nonneman of Montana.
The Associated Press Contributed to this report.