We were warned against going to Chiapas because the Zapatista guerillas were waiting ... guess what ... we never saw one!
From Wikipedia -
In the late 20th century, indigenous peasant farmers grew discontented with the Mexican government for having long given less attention to their poor and largely agricultural region than they preferred. A chief complaint was that many indigenous farmers were required to pay absentee landlords, despite repeated government promises of agrarian reform. Article 27 of the constitution of 1917 guaranteed indigenous peoples the right to an ejido or communal land. After the financial crisis of 1982, Mexico restructured its economy and de-prioritized land reform (long since completed in most of the country). The government of President Carlos Salinas de Gortari sought to liberalize Mexico’s closed economy. As part of this process, Mexico repealed the constitutional guarantee of communally owned ejidos for rural communities. As the North American Free Trade Agreement came into effect on in 1994, indigenous Chiapanecos felt increasingly left behind.
Such disaffection led to the rise of the Ejército Zapatista de Liberación Nacional (EZLN, “Zapatista National Liberation Army”, commonly called the Zapatistas), which began an armed rebellion against the federal government on January 1, 1994 as a response to the implementation of the NAFTA. Zapatista rebels are mostly Tzotzil and some Tzeltal Maya, from the central highlands of the state, and the group’s spokesman, the Sub-Comandante Marcos, gained it international attention.
The group is named after Emiliano Zapata, iconic general in the Mexican Revolution of 1910, who is lionized for having defended the rights of poor farmers. Although the EZLN was in principle a peaceful movement forced to arms by the Mexican government, to guarantee the right to ejidos, there were a number of violent episodes in its history. The movement began in 1994 with the seizure of four cities (most notably San Cristóbal de las Casas), over 600 ranches, and control over about a quarter of the state.
After pushing the Zapatistas out of San Cristóbal, the Mexican army kept them bottled up in their jungle strongholds, cutting them off economically and politically. The Mexican government installed a solidarity program which while “ostensibly designed to alleviate poverty, […] instead became an instrument for rewarding political loyalty and contributed to the anger and frustration expressed through the Zapatista rebellion.” In 1996, both sides signed a peace accord.
Meanwhile, landowner-funded paramilitaries sporadically repressed indigenous communities. A series of massacres ensued, typified by the 1997 Acteal massacre, where 45 indigenous refugees, mainly women and children, were killed in a church.
In 2000, the EZLN renewed its resistance, autonomizing a number of jungle villages and sending a delegation to Mexico City. While the delegation did not obtain everything it sought, despite some support from President Vicente Fox, the villages remain under Zapatista control. In August 2003, the EZLN declared all Zapatista territory an autonomous government independent of the Mexican state.
The armed EZLN has mostly eschewed armed conflict, in favor of political efforts to build health clinics and schools in their communities. Anti-Zapatista paramilitary and military activity continues on the part of the Mexican government, however, threatening re-escalation. Zapatista action continues now with the implementation of the Sixth Declaration of the Lacandon Jungle and the launching of The Other Campaign.
In order to mitigate the problems with the increasingly disaffected and rebellious population in Chiapas' Lacandon region, the federal and state government designed multiple social development programs. Many of these were criticized for being counter-insurgency projects, aimed at controlling and pacifying the indigenous population, rather than investing in their development and listening to their demands. Some of these programs include Plan Cañadas, PIDSS, and Prodesis.