As of last year: We were told by Amtrak, that Coach USA met all trains at the Orlando station. Even if your train is late, they will be there. After you arrived, arrangements can be made with them for transportation to any Disney property. You pay at that time. They are similar to MEARS transportation at the airport. We did use Coach USA and had no problems with them. Our train arrived several hours late, (the Sunset Limited!) and they were waiting for us. They also give you a number to call if you would like a return trip to the station.
Enjoy the train! It's our favorite way to travel.