Why did Spain become intolerant towards the Jewish and Muslim religions from the 14th century until the 16th century?

There are numerous reasons for Spain's intolerance towards these groups during this period. Both Jews and Muslims were widely viewed as enemies of the state. This view enabled the Spanish monarchy to strengthen its power and crush opposition. Antisemitism has a long history—both in Spain and elsewhere—and it became particularly virulent during this period. Antipathy towards the Muslims dated back to the Crusades, which began in 1095. Another reason for the brutal suppression of these groups was the tyrannical tenure of Tomas de Torquemada (1420–1498) as the Grand Inquisitor of Spain.
Between the 11th and 14th centuries, Christian Europe was preoccupied with the Crusades. The goal was to retake the Holy Land from its Muslim occupiers. In the end, the Christians failed. The hostility between Christians and Muslims did not end with the Crusades, however. The centuries-long Crusades inculcated religious intolerance in Christian Europe. War against Muslims continued both in Eastern Europe and in Spain. In fact, the war against Muslims in Spain did not end until 1492.
Muslims had lived in and ruled southern Spain for centuries prior to 1492. For centuries, they had lived in harmony with both Christians and Jews. Remnants of the once-vibrant Muslim presence are evident in places like Alhambra, a fortress and palace in southern Spain. As Christians gained ascendancy on the Iberian Peninsula, religious tolerance declined. The beginning of the Spanish Inquisition in 1478 was the death knell of the Muslims and Jews.
Antisemitism predated the onset of the Spanish Inquisition. The Jewish community had thrived and prospered in Spain for centuries in spite of intermittent outbursts of antisemitism. In 1391, there was a pogrom in Spain, and Jews were pressured to convert to Christianity: baptism or death. Those Jews who converted became known as conversos. Even conversos were widely viewed with distrust by the authorities.
Muslims, too, had to convert or suffer the consequences. By 1500, there were few practicing Muslims left in Spain.
This era of intolerance and rising Spanish power set the scene for Torquemada. He became confessor and adviser to Spain's rulers in 1483. His power was immense, and torture was widely practiced. He persuaded Spain's government to expel all Jews in 1492. Many were killed in what amounted to a genocide. Property of the accused was seized. Torquemada was so vicious that the Pope tried to restrain him.
The persecution of Muslims and Jews is a sad and tragic chapter in Spain's long history.