“The article makes it sound like it’s local governments doing the persecution, not the Mexican national government.”
And where in the article does it say that the Mexican national government is doing anything about this?
The article suggests (not implies) the opposite:
With the local government is running cover for the persecutors, the national government will need to intervene. However, given the state of Mexican politics and the influence of the Catholic faith in Mexico, that doesn't seem too likely.