Paranoia's a Decade Behind Reality
The up and coming thing in railroading is "Communication Based Train Control" where R/F links replace most trackside signals. This is not easily hackable but there's been an amateur project that uses the data traffic to get a real time picture of trains on a particular section of track. (Think of it as the next step up from those real time transit displays.)
If you successfully hack these links then you can potentially cause trains to collide. Obviously someone will likely notice what's going on and issue verbal orders to train crews but this is probably worth a bit of paranoia to the professional paranoids.
BTW -- The UK is experimenting with this on a section of track in North London. I think the plan is to extend it to the East Coast Main Line. The prototype area has actually had the trackside signals removed.