The whole story is not being told. This is an old problem and is not just religious but based on political and ethnic problems as well. Incidentally, the Catholic Church has tried to help:
*On August 27, 1998, indigenous Catholics in Mitziton, Chiapas, took 23 evangelicals hostage and threatened to eject them from the community if they did not convert to Catholicism. Catholic and state authorities intervened to obtain their release. *
But Catholics have also been victims:
In addition, a number of Catholic churches were burned in Chiapas, but the authorities made no arrests. *The Catholic Diocese of San Cristobal de las Casas, Chiapas, has complained that progovernment armed civilian groups threaten and harass its lay catechists. Moreover, human rights groups allege that such groups have murdered five catechists from 1994 through 1997. Nonetheless, the motive for these killings has not been established, nor has anyone been apprehended or charged. The Diocese also has alleged that these groups have vandalized 28 Catholic churches in Chiapas and caused more than 20 other churches to close. Church closures occurred when local indigenous groups physically prevented Catholic catechists from occupying and opening existing churches, with the active or tacit support of local officials. *
From: U.S.Department of State
Annual Report on International Religious Freedom for 1999: Mexico
state.gov/www/global/human_rights/irf/irf_rpt/1999/irf_mexico99.html