I don't believe they have any choice. I imagine that seriously resisting the TSA, no matter how justified, would result in much trouble with their military superiors. Bad fitness report at the least, don't know if it could go as far as a court martial, but offenders would certainly be in the crapper as far as their military careers are concerned.
And therein lies a fundamental shift in power to Obamamugabe's misnamed "Homeland Security" civilian thugs. As civil liberties are shredded, the military will do nothing to protect the citizenry from a rogue C-in-C.