Security and privacy are not opposite ends of a seesaw; you don't have to accept less of one to get more of the other. Think of a door lock, a burglar alarm and a tall fence. Think of guns, anti-counterfeiting measures on currency and that dumb liquid ban at airports. Security affects privacy only when it's based on identity, and there are limitations to that sort of approach.
Since 9/11, approximately three things have potentially improved airline security: reinforcing the cockpit doors, passengers realizing they have to fight back and -- possibly -- sky marshals. Everything else -- all the security measures that affect privacy -- is just security theater and a waste of effort.
And a waste of money.