Thomas Jefferson was a dilemma. On one hand he owned 187 slaves (52 from his inheritance and 135 from his wives' inheritance) and on the other, he supported emancipation and abolition of slavery (in an original draft of the Declaration of Independence, he decried slavery as it violated "sacred rights of life and liberty"). He was not cruel and was rather liked by his slaves. He viewed the black slaves as inherently inferior to whites, in terms of skin color, beauty, reason and intellect. However, he believed them to be equal to whites in terms of memory and superior in terms of musical abilities. He was of the opinion that blacks and whites cannot mix and as such believed that rapid emancipation would ultimately lead to clashes between the races and genocide. He favored slow emancipation and a return of blacks to Africa (either to their native lands or to a new all-black nation).
Some of these views (lack of intelligence, reason, imagination and oratory skills) can be thought of as a result of the long-term oppression of blacks, who had no formal education and/or motivation. All of these ideas have no scientific basis and are strongly correlated to the treatment received by blacks at the hands of the whites. His thoughts on slow emancipation, the idea that slaves may not be ready for immediate integration into society without any formal transition, might have been a logical one, although it regrettably does not support the idea of total freedom. His fears of interracial clashes and eventual genocide are (hypothetically) the result of causality—consistent with his views on inferiority of the African race. He does not incorporate the idea that (if needed) blacks might improve their educational level and standing in society and become equal to the whites. So, his views show some conflict between correlation and causality.