In my opinion the problem here was (its a done deal the tracks are already in place so the damage is already done) the way it was done. According to Mexican law you have to do environmental impact studies before this kind of projects. This was skipped, so the project was stopped by the courts. In a power play AMLO declared the train important to national security and forced the project trough building it using security laws and using army engineers to build the project under project management of the Mexican army. This way the project skipped all the environmental studies needed to actually do this in a sustainable way and bypassing the juridical system. So this is why people are complaining about environmental impact of a train even if the train itself have pretty low carbon emissions per passenger, how its build impact the environment.
Im not one of those that complain to much about the pillars under the track as i think its more important that the train when its first get build will not collapse into the cave. Its ugly as **** and its is the prize we pay for the ugly business of mass tourism.