Reading the actual DHS info on this not the chicken little version it looks like DHS doing this to prevent suits against the airlines and gov't by the ACLUeless.
Currently airlines have to check passengers against a gov't watch list.
The new rules would establish a system where the gov't checks the airlines passengers against the gov't watch list.
Under the current system airlines could be liable it they screwup someones name and that passenger is incorrectly determined to be on a gov't watch list.
TSA: Secure Flight Program
In other words, y'all can thank these guys:
American Civil Liberties Union : Fact Sheet: Federal Watch Lists
This is a case of be careful what you wish for I am thinking.