It is definitely hard to disrupt Large Trains. I've been practicing doing it several different ways and had little success, but I have found a method that may help:
Subtargeting. I'm still not as proficient at this as I'd like to be, but generally players leave the default turrets or upgrade them on their Large Trains, this allows you to pick a subtarget such as a turret mounted directly in front of one of the two engines. As long as you fire the disruptor fast enough, it should connect and bring the Train to a juddering halt. Though flicking through subtargets can eat up time and as soon as the Train begins facing the other way to you, it's normally too late.
I'll quickly explain why this is slightly more effective: Basically the reach of the disruptor missiles blast radius is too small to clip the Large Train's engines when it makes a hit, as the missiles by default home in on the centre of the Train. Firing from behind, this would cause the missile to hit the cargo pods at the back, even further away from it's intended target. If you can get the Train's front mounted engines in the blast radius, you should be able to stop it cruising.
An alternative is to "camp" a well used route and try to hit the Train directly in the face. Neither of these methods is fool-proof and it takes a lot of trial-and-error to get them right, but it can be done.
While we're on the subject, I'd like to recommend a few things regarding Train Cruise Disruptors- first off, the projectile speed is slow enough that if a Train is up to speed (ie: 350m/s cruise) the disruptor missile can't catch it. I'm fairly sure this isn't a problem with other disruptors as they're specifically designed to catch cruising ships. Another thing- price. For the percentage of success you do get from disrupting Trains, the current cost of missiles is outrageous. Especially considering the idea is that they're used in order to make a profit from pirating.
One last thing, has anybody compared the Mosquito to the Train Disruptor? I'm unsure of the differences between the two.
From the quick I took of the stats, the difference is speed and blast radius and possibly turn rate.
Though the train disrupter stills says the same blast radius as the other cruise disrupters at the minute, the infocard says the radius has been increased but not by how much.
edit:
Ok, just to see what would happen I took the shield of my large train.
Any NPC with a wasp cruise disrupter can stop me, regardless of where the missile hits.
So it appears that the shield is what is stopping the original disrupters from working.
So either the shield shape needs to be altered/looked at or we remove the shields from all transports and trains.
Before I get lynched for that last suggestion heres why:
1) you'd have to use a frieghter/armoured transport to trade in the borderworlds, mainly because they have shields, CM droppers, more weapon mounts and they have a massive number of weapons to choose from.
2) traders would need an escort in most systems without tradelanes, this means an escort faction would be able to exist and it would increase RP possiblies.
3) we can scrap the shield battery supply and then double the nanobot supply, meaning that the transports and trains can survive longer even without shields.