Nowadays two companies run freight trains in the top half of the country, but there are no passenger services, unless one counts a few small tourist lines (e.g. through Copper Canyon, another in Yucatan…). People generally get around by bus, car or plane.
Looks like this is set to change, however. Construction has just begun on high-speed passenger lines from the capital to Toluca and Queretaro, with further services to Puebla and Guadalajara to follow.