You can take the train from FCO to Civitavecchia, but you'll have to change trains in Rome. The trip is between 1.5-2 hours total, depending on the connection time. I think the fare is around €10 each way, maybe a little more now since the last time I looked into it was a few years ago. The big advantage of the train is the ability to avoid traffic, which can be very bad during rush hour.