It's not like some crazy terrorist with a boxcutter is going to force his way into the locomotive of an Amtrak train to hijack it and ram it into a building.
Make transit safe? It's NEVER been safe. Trains hit cars, or each other, and people die, ALL THE TIME. Next time some crazy guy who wants to commit suicide parks his car on the tracks, then changes his mind and runs away at the last minute, derailing an LA commuter train and killing a bunch of people, is the plan to try him as a terrorist, rather than just for, say, 2nd degree murder? Yeah, that will do a lot.
Hey, maybe they can put anti-terror squads on the New York subway and get rid of the muggers. Yeah, sure. Just the way that tracking the checked bags to the passengers on planes keeps your luggage from going to Denver while you go to Chicago. We all know how successful that one has been. Maybe a guy in a beret will ask for "Papers, please," before you can get on a Greyhound bus.
Or maybe the ultimate plan is to make the trains run on time.