I'm pretty sure that was the NYPD. Unlike the TSA searches, you can refuse to comply with those.
https://www.wsws.org/en/articles/2013/08/10/vipr-a10.html
http://www.nytimes.com/2013/08/06/us/tsa-expands-duties-beyo...
(Side note, who the hell comes up with these names, and why hasn't somebody with some experience with marketing and PR talked to them?)
Oh, they have it. You're just not the TSA's customer.
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Rail's handling of TSA should be a model
http://www.cnn.com/2012/02/06/opinion/don-phillips-tsa-vipr-...
Besides, they'd probably comply willingly. The airline companies and airports do; hijackings just ain't good for business.