Liner notes to a Neil Young compilation state this 1975 song was banned in Spain.
There is not too much definitively known about Conquistador Hernán Cortez (1485–1547). We know he took over Mexico for Spain in the 1500s, which meant the fall of the Aztec Empire there. Young calls him a killer, and a destroyer of a peaceful civilization.
This is simplistic; there were Aztec wars. Young may be making a more general statement against imperialism and colonization, and besides, leaves most of the room in the song for his guitar solos.
Related: Procol Harum – Conquistador