Airport security is problematic. The lines are long and unfair, and once you get to the screening area the rules are inconsistently enforced. The potential new head of the TSA has some sound ideas about how to improve air security and move away from the inefficient system we currently have. I think we can all agree that "intelligence-driven security" sounds better than what we endure currently.
Over the long term, airline/airport security will improve one way or the other, and security for other public modes will likely increase. There have been a number of transit attacks over the past few years, the most recent one in Moscow. At some point these attacks will lead to increased train security. There are already regular security exercises in large transit systems. This will reduce whatever perceived advantage trains and transit have over air travel. More importantly from a policy perspective, we shouldn't assume that security measures are fixed over time. They evolve as we (hopefully) get better at it.