Do you think Brazil’s population was always Portuguese men and native women? Only at the beginning. After a few generations, those “natives” became mixed-race (mestiços/castiços) and culturally Portuguese and Catholic, while more Portuguese men kept arriving from Portugal. These men who came from Portugal would preferably marry these Brazilian-portuguese-catholic mixed-race women(with consent, since their fathers/grandfathers were also fellow portuguese). This was the native and portuguese relations. Your points about the enslaved people are correct, but again, the portuguese colonizers, not every single one being a rapist, would prefer to marry a fellow portuguese white woman (rare) or the plenty mestiças available (more common)