Rail travel has a certain romance that cars, boats, and airplanes can never quite capture. I love listening to the sounds, meeting different types of people, reading the rail maps, and waiting on platforms. I think I fell in love with the trains when I served as a missionary in Australia. Sydney has a great rail system, and even after riding CityRail frequently for almost two years, I relished the experience of planning my journey, finding the right platform, mingling with the people, listening to the clack of the tracks and the conductors' whistles, and rushing in before the doors closed. Riding the train was a welcome respite from walking or biking (although we often took our bikes on the trains with us), and the fare was definitely worth it, considering the large areas we covered. We never had to travel too far, because we stuck around Sydney, so I can't say we had vacation-type train trips, but there were some days when it was necessary to spend a significant portion of the day on the train, and it's a great way to travel.
To compare with the other options mentioned, train travel offers great views of the places along the way. Enjoying the journey is important. It is nice to go for journeys of less than a full day on a train. I think for longer distances, planes are obviously more practical. I am not big on boat travel, although I love the ocean. I would rather stay near the shore and enjoy the curiosities of the beach.
With all things considered, including the threat of terrorism, I would still say that transport through planes is the best mode of transport.
All the other types of transport can still pose a safety threat, as the blowing up of a London bus by terrorists prove.
The only draw back that I see to air transport is the amount off checking in time that you have to allow for, which is worthwhile if you are going on a long journey, but not quite as worthwhile if you are only going on a short trip.