I've never been accused of being a liberal, but this is one area where any liberal who opposes this system is right on the money.
It's possible that this system will be used to dragnet for criminals , much like the often-used example of the DUII checkpoint. The legality of using CAPS II as a system to catch or flag criminals unrelated to terrorism would be challenged under statutes governing probable cause. If a person is arrested for an outstanding warrant on traffic fines when trying to fly, his attorney would have a field-day since the crime he was arrested for did not pertain to the subject of the search. When a search warrant is issued, it must clearly state what the search is looking for. Broad search warrants are not allowed, and if they are issued too broadly, they are overturned in court and the finding are often ruled inadmissable. Acting on the finds of such a search for reasons of a traffic fine or even serious crimes not relating to terrorism would not be legal, because the scope of the search is too broad. Thus, to arrest a person on the basis of these findings would be essentially a warrantless search that has not been subjected to judicial scrutiny or prudence. Simply buying a plane ticket does not automatically give consent for a search beyond the scope of reason (ie. bags and personal items), any more than possession of a driver's license waives any rights we have for a search during a routine traffic stop.
I have heard it said that a conservative is a liberal who has been robbed, but a libertarian is a conservative who has been arrested.