I too had some trouble trying to get the train to run, read the instructions on how to operate it, and it will tell you how to get the train moving.
I found the instructions just a little bit unclear, so I kept trying, so what you need to do is first push the Delete key, you should hear the key being inserted. Then push Page Down 3 times to activate ATO mode. You should hear the chimes. At this point close the doors, and the Blue light should come on. Make sure the gear is set to F (forward) and power set to N (Neutral). Hold down the 5 and 8 keys at the same time until the train starts moving, then you can let go, and the train will move. The instructions say 3 seconds, but for me once the train starts moving, you can let go like a second after that. At this point all you need to do is open the doors/close doors at stations and hold down the 5 and 8 keys to get moving again.
If you want to run it in manual mode, push delete, then Page Down twice. Then tap the space bar. Close the doors, and you should be able to control the train manually, you will still need to follow the speed limits, as it will force you to if you go over.
Hope this helps.
Also if you want to know if the plugin is working hit F10 to open the debug menu, you will see the status listed on it. There was one time where the safety systems didn't work at all though even though it said the plugin was loaded, I just restarted the game and it worked agin.