This is a simple person's simple understanding.
The american lack of immunity to european communicable diseases was probably the decisive factor in their domination. Once introduced, the diseases moved much faster than europeans via the extensive american trade and communications networks. Eventually, european "explorers" they were walking into regions where the population was already severely stressed if not devastated by diseases. The vulnerability of americans to diseases was an advantage exacerbated and exploited by every means, no matter how brutal or devious.
So, a few kingdoms in europe began to accumulate wealth in a way previously impossible. They were motivated to engage in the whole project because their ruling classes envied the luxury goods available elsewhere in eurasia. But they had nothing to trade. All the cabbage in europe couldn't buy single bolt of silk. To say nothing of spices, tea, and other goodies. I don't know how the trafficking of african people first got started, but the benefits of bringing people who were completely disoriented, stripped of social context, and also a bit more resistant to those diseases became evident. But without the depopulation enabled by epidemics, it wouldn't have made sense to bring in a whole new population, much less two new populations (africans and europeans to keep it simple). And no matter their depraved aspirations, europeans would never have been able to defeat the many american nations on a more equal military footing, without the immunological advantage.
One other thing about agriculture, is that the american landscapes were intensively managed for thousands of years to produce what humans needed. Europeans were often oblivious to the sophisticated agricultural technology, as it did not resemble the "farming" they were accustomed to. So they didn't recognize the extent of the interventions which had produced to the "garden of eden" they conquered. While things eventually unraveled due to the maintainers being murdered, displaced, or otherwise prevented from keeping things up, the europeans often wandered into environments which "nature" had provisioned with a bounty of goods, there for the picking.

