Seeing a train in s3 is interesting. Most likely, it's just been sitting there for 200 years and isn't actually being used. However, if it is in use, the NCR is really the only faction that we know about who has running trains.
Back in New Vegas, Colorado was Legion territory, and I highly doubt that the NCR is there, it's too far away. But the showrunners also hinted that the Ghoul might not even make it to Colorado, so it could be somewhere else, like Utah. It's also possible that the railway lines in that part of the world were pretty undamaged in the war, so organized wastelander groups can actually use it.
