Answer: European diseases had killed much of the native workforce.
The fact that many natives died due to European diseases was an important reason why Spanish plantation owners used enslaved Africans instead of enslaved natives.
However, another very important factor was that the Spanish monarchy considered native people to be "vassals" of the Crown (the modern-day equivalent would be citizens of Spain). Therefore, as they were subjects of the monarchy, they were considered to be full-fledged humans, and could not be enslaved. This was the case since the passage of the New Laws in 1542. Although natives were often abused and mistreated, this protection made it harder for plantation owners to enslave them in large numbers.