Like many features of the original constitution, protecting slavery (the slave states were modtly low population states, with even smaller voting populations, and were particularly concerned that equal representation would eventually turn against them—abolitionism was already a thing at the time of the Constitution, and they were very concerned about it taking hold) was a major concern. The representation structure (and it's special protection against revision by amendment) plus the 3/5 compromise plus the explicit, limit term, protection of the slave trade, among other provisions of the Constitution, were protection against that eventuality.