Spain founded 23 universities in colonial America, something without parallel in History
Culturally speaking, Spain gave the very best to America. “The Spanish record of some twenty three colleges and universities in America, graduating 150,000 (including the poor, mestizos, and some Negroes) makes, for example, the Dutch in the East Indies at a later and supposedly more enlightened times, look obscurantism indeed. The Portuguese did not establish a single university in colonial Brazil nor in any other overseas possessions. The total of universities established by Belgium, England, Germany, France and Italy during later Afro-Asian colonial periods assuredly suffers by any fair comparison with the pioneering record of Spain.” (American History professor Philip W. Powell)
The rest of the History
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Good history, done with consideration and taking into account the judgements and morals of that contemporary society, is almost never the black and white of much of current 'knowledge!' Shades of gray from white to black as we see the trend of various forces and societal movements played out on the stage.
Few people today understand the 700+ year "Reconquista" of the Iberian Peninsula and its effect on the Spanish and Portuguese societies and only decry what they see as the crimes against the Moriscos and the Jews lumped under the "Spanish Inquisition" and other actions. Having the gift of the "New World" following the end of Moorish Spain did give what seemed like God's gift of unlimited wealth and eternal prosperity to those shared countries as reward for their long struggle. These Universities you cite were some of the best of the results indeed.