Hi itsmee. I have been travelling on trains to work for 18 years now, and I went through a phase, not of being scared of the train, but panicking at the thought of "what if I am sick on the train? What will people think?" That thought process would have the effect of making me feel sick or faint, which of course, heightened the risk. A couple of times I would be standing in the train, unable to get off, and having to endure this panic attack. It would usually end with me breaking out into a cold sweat, after which I felt normal.
I didn't take anything for this, neither did I see a doctor, but I am sure it was just psychosomatic. It went away, funnily enough, after I got married and settled down, so maybe the panic attacks were really a symptom of unease in my personal life.
Try taking your mind completely off the journey by reading a good book. Remember, hundreds of thousands of people travel by rail every day without feeling sick - think to yourself "why should I be an exception?"