Railway transportation was used by both GDI and Nod in the southern United States theater of operations, early in the Second Tiberium War. One mission during that war saw GDI forces under the command of McNeil had captured a Nod train station that was being used to evacuate artifacts from a crashed Scrin ship. The train that the GDI forces captured was later destroyed by a Nod defensive fortification (laser defenses) on the east end of a railway bridge in the next GDI mission. Few Nod mission in second tiberium war involve capturing or disabling trains to extract important person. The universe saw that many railway lines have been disabled due to changing of earth texture (credited to Tiberium investation).
Modern high speed trains are used still today in favor of hybrid electric/fossil fuel powered cars and fully electrical powered cars. This is due to the fact that GDI wanted to preserve what's left of the atmosphere by cutting green house gas emissions and pollution caused by fossil fuels and also to the fact that cars are very few in number and very expensive. Trains are good for fast redeployment of troops and equipment in many theaters of operations during TW2, were not armed or armored enough to withstand an assult from Nod or GDI forces. The railways were also used in the Generals Universe.
The timeline in Command and Conquer Generals saw railway technology still based on old railway technology, even steam locomotives is still used widely. The railway might be significant in few missions, from deploying troops to stopping enemy deployments. It is noted that the railway is durable enough to handle extreme cargo such as Chinese Overlord and orbital rocket. In comparison, Tiberium Sun saw much more advance, but less durable, design. It may be considered as using MAGLEV like technology and quite speedy, although banning vehicle transportation using it. On both universes, trains on the move represent significant hazard as they are capable to rip almost anything in their railway.