Context: During 16th and 17th century several Popes made proclamations to the effect that "slavery is bad" especially on Christians.
Slave traders involved in the Atlantic trade were quick to adopt the newfangled idea that all of humanity can be divided into "races" based on skin color and physical features. Africa was their largest source of slaves, and if they could convince everyone that African people were somehow not fully deserving of (what at the time passed for) human rights it would mean extreme profits.
The cross logo belongs to the Portuguese royal monopoly Casa da Índia and is a bit anachronistic since the slave trade was fully privatized by late 1500s