Just some unsupported anecdotal impressions:

The commuter rail traffic in the BoshWash Corridor is handled mostly by "locals", owned and operated by regional or state transportation authorities. Most of my experience is with NJDOT on the Trenton-NY run (which shares rails, by lease, with the Amtrak tourist lines), and with SEPTA (SouthEast PA Transpo. Auth.) which inherited the old Reading RR and Pennsylvania RR commuter rail lines into Philly from various suburbs.

The trains make frequent stops in a variety of stations of wide-spread age, condition, size and passenger base (that is, usage per day). Standardizing them to some common level of security would be nearly impossible, and that's just from a architecture/engineering standpoint. Their riders sometimes arrive at the very last second (running for the train as it's pulling out is not just a 1940s movie cliche)... if they were able to find a place to park.

The kind of additional roadblocks to rail travel - which is barely efficient as it is - that S_M sketches in his post would actually protect commuters from being bombed... it would drive them away from using the trains, which would then stop running. Permanently.