With many modern aircraft, they cannot be flown manually, with the stealth planes for example they are so aerodynamically unstable the computer system has to keep constantly changing the flight surfaces rapidly to keep it flying, this was true of the F14, and is true I believe for other fighter aircraft, and from what i recall is true of the modern generations of Jet passenger planes and the like. Basically, the pilots settings are translated by the computer systems into changes to the flight surfaces or things like the throttle, often making a lot of adjustments rapidly to keep it flying true to where the pilot wants. You could, if you could get to these systems, hack into them and cause a plane to crash, so it isn't like we don't have vulnerable systems now. One of the things to keep in mind when comparing systems that routinely get hacked to something like an autonomous train system or let's say an autonomous piloting system, like things like aircraft that depend on computer flight systems (especially military), when these systems are designed that kind of security is going to be a major part of the design, because they could be vulnerable. The systems that are hacked today are in many cases because they had security added on to them, or are systems where those running them didn't have the attitude that security was a big deal, enough that it allowed things to slip by (for example, the Anthem hack may have been the result of employees clicking on a phishing email, which indicates the company didn't have very strict standards with mail (where i work, outside mail has links disabled, and if you want to actually try and open it, you have to cut and paste the link; not to mention they monitor email, have all kinds of training on computer security including phishing awareness, and run phishing tests with real consequences if people end up clicking on them). Other companies get hacked because things like accounts with root level permissions (in Unix) are visible, and where passwords are in non encrypted form when they hack customer accounts. When you are talking about something like a train control system, they are going to be a lot more vigilent, because the awareness is there and security is now being routinely designed into systems.
Does that mean autonomous train control is a good thing, is getting rid of human operators smart? It is going to come down to, like most business decisions, based on the benefit versus the risk. If such a system has a major accident, they know that it is going to bring all kinds of things down on them, from those saying "I told you about them newfangled computers that crash" to the lawyers jumping all over them, and even the thought that let's say congress might indemnify them could flop in the face of public outrage. If they feel they can create a system that is safer than human operated trains, they may well do it because of the efficiency and cost savings, it is the way decisions are made.
I have my doubts they will go to driverless trains anytime soon, at least not on mainline railroads, not because of technology but because of the backlash to it. Like driverless cars and trucks, there are a lot of issues not necessarily related to the technology that likely will delay it for a while, but the profit motive has shown with many things that as the Borg used to say on Star Trek "Resistance is futile". I am not proposing it as a panacea, nothing is, just pointing out that the 'powers of the marketplace' are a strong force, and cutting labor cost/increasing efficiency and productivity is a major goal of most companies, and automation can do that, but it certainly also has its drawbacks. The car in many ways was a major benefit over horses (I remember recalling that the NY Dept of Sanitation used to remove something like 6 million pounds of horse manure from the streets of NYC around the turn of the 20th century) but it brought issues of pollution and other kinds of issues (vehicular deaths) with it, too.
A PTC system is a needed step in all this, an autonomous system likely would need the PTC system to keep track of other train traffic and also be able to be controlled in case something in fact went wrong (like PTC telling it that track was washed out ahead and to slow down while it was being diverted to another track or told to pull into a siding and wait). A PTC system itself could obviously be a security risk, if PTC can override a human engineer and slow the train down or stop it, it could be used to do serious things to the train, too, so the threat of hacking is already there.
