Why there is no why .
Attempts to identify causes in a genocide often risk to reduce it to almost an inevitable product of the circumstances. Historical contexts can help understand why a certain type of violence can happen, but in no case offers moral justifications.
In the case of the Maya genocide the "occasion" that lead to its taking place was the context of the Civil War. In this years, the Guatemala government, responsible for the crimes, has had the support of the United States, beginning with president Eisenhower. The US financially aided the Guatemala government and its Army as part of their international policy strategy in the years of the Cold War. This collaboration was confirmed in 1999 by President Clinton. (http://www.guardian.co.uk/world/1999/mar/12/jeremylennard.martinkettle)
The aid offered by the USA wasn't limited to money. Members of the Guatemala Army received extensive training by CIA in the counter-insurgency practices that were used. Furthermore:
Christian Tomuschat, the German jurist who headed the panel [of the CEH], said, ''The United States Government, through its constituent structures, including the Central Intelligence Agency, lent direct and indirect support to illegal state operations.''
In the Civil War the State implemented an anti-communist ideology to fight the guerrilla groups. This ideology however merged with feelings of racism and with the deep segregation against the Maya that had been present for centuries. The violence in the rural areas therefore, even if targeted against the indigenous populations, was concealed as a fight against a supposed communist insurgency and as a series of measures for national security.