I've always loved traveling on trains, but to climb between clean sheets on a comfortable bed aboard one of them gives me an almost sinful feeling. I know it gives me sinful thoughts. One of my favorite routes aboard one of the Ferrocarriles sleeping cars was the Veracruz line. From Mexico City it would allow me to come to life in the morning with the train going at a leisurely pace through the plush landscape outside of Veracruz. Mazatlan has both, plus easier access.
Physical security is no problem on board the passenger trains of any class service.
I never met anyone in person who has ever been assaulted. Though I did get a couple of first hand stories of stolen baggage aboard second class trains. Nobody, including the conductors were happy with these delays. As with a lot of things there is usually more than one reason for actions such as these by the Mexican government. This can be a dangerous proposition however as the bushes along side the tracks are usually only trimmed by the passing trains themselves.