The point is that planes are only a high value target when they can be used as a missile. If the cockpit is locked from the inside then this possibility goes away. Even with a bomb on board no one will give control to someone who may use the plane as a missile.

There is no more incentive for someone looking to cause mayhem to blow up a plane than there is to blow up a shopping mall or any other building with more than ~180 people inside (the approximate number of seats in a 747).