I read an article on the BBC about the pope canonising a certain Junipero Serra who is loved by the Hispanic community but not really liked by the natives, so my question is why is he so controversial?
Fr. Junipero Serra was one of the Spanish missionaries who helped Spain maintain a presence -- if not an empire -- in the American Southwest. This was at a time when the Spanish government provided less support to Spanish in the region than, say, the British did to its colonists in the 1600s and 1700s. Today, there is a mission in San Juan Capistrano that he founded, as well as a Catholic school in the area that bears his name
The controversy rests on the nature of the relationship between the Spanish and the Native American population, and Serra is viewed as being complicit in this. The Spanish used a labour system known as the encomienda, under which a Spanish encomendero provided protection and Catholic instruction to natives in exchange for property rights over the natives, allowing their use as a captive labour force. A recent article in the Economist describes the other perspective on Serra:
For others the sins overseen by Serra are too deep for him to be so exalted. At the San Gabriel Mission, in Serra’s day a bountiful source of produce for the young city of Los Angeles, a painted sign from the 1960s welcomes visitors to a “garden of peace” where trod “the daring Redskin, the blithe-spirited Mexican” and “valiant Spanish soldiers”. Modern plaques record that 6,000 Indians lie beneath the grape vines and flowers, many killed by disease, and that local Tongva Indian culture was almost wiped out. Indians were often paid for their labour with glass beads. They were flogged for disobedience or “concubinage” and—once converted—were not free to leave. Deserters were hunted down and beaten or chained. Serra sorrowed over excesses but supported floggings, which he likened to stern parental discipline.
Instances of violence also marked the Spanish conquest of the American Southwest, such as a revolt by the Pueblo in 1680
Sources:
Timothy J. Yeager (1995). Encomienda or Slavery? The Spanish Crown's Choice of Labor Organization in Sixteenth-Century Spanish America. The Journal of Economic History, 55, pp 842-859. doi:10.1017/S0022050700042182.
The mission system in California created or coincided with a massive decrease in the population of Californian Indians, which some people blame directly on mission conditions. But I'm unsure how much of this can be directly attributed to malice or mismanagement by the Spanish authorities in particular. The Native American population of North America as a whole did not start to rebound until about the year 1900.