Jefferson, to the best of my knowledge, never thought the races were totally equal, but, it's possible he became more racist over time. Fergus M. Bordewich, author of "Bound For Canaan" seems to vaguely imply Jefferson might have moved towards heavier racism due to frustration of seeing slavery continued in practice. Here's what Bordewich says, in full:

"Jeffersons racial dilemma, in all its dimensions-moral, psychological, emotional, political,-was very much that of nation itself in the early years of the 19th century. No American of his time examined his own ideas of more seriousness and Jefferson, process that has been recounted with thoroughness by John Chester Miller, in the Wolf by the Ears: Thomas Jefferson and Slavery. In his struggle, and ultimate failure, to find a resolution to the problem of slavery, the uncertainties of young nation can be seen as a no other single mind. From the grinding stress of that ambivalence would grow the inspiration for the abolitionist movement, and it's activist cutting edge, the Underground Railroad, as well as the most bigoted defense of slavery, and the political philosophy of states' rights.

Jefferson embodied the very best in a nation that was increasingly struggling to find a painless way to end slavery, an effort that was doomed to failure from the start. He had, as much as any man living, created the United States, crafted the principles by which it strove to live, and been a part of the compromises that has been necessary to bring the country into being. More than most, he believed that slavery was morally incompatible with white men's freedom, and ultimately a reef upon which the nation might someday founder. In later years, his idealism, like that of many of his generation, would atrophy. Despite protestations to the contrary, he would eventually slip uncomfortably close to the camp of those who embrace slavery and state's rights as pillars of American stability. Yet his clarion appeals for liberty, which are most memorably enshrined in the immortal words of the Declaration of Independence, would have an impact far beyond his ultimately class-bound intentions."

Jefferson surely hated slavery, and was quite furious when his 1784 plan to the Continental Congress to ban slavery in all western territories, south and north, failed by one vote. He wrote of the matter:

"Thus, we see the fate of millions unborn hanging on the tongue of one man, and heaven was silent in that awful moment."

However, Notes on the State of Virginia, which came out in 1787, had a lot of racist remarks, like the foul of odor of blacks, and the thought the whites were certainly intellectually superior to blacks.

From what I understand (and someone correct me if I'm wrong), Jefferson (like many early abolitionists, including those who worked on the Underground Railroad) never believed that the races were completely equal. Believing that blacks were inferior to whites in one manner or the other, yet still opposing slavery, was quite the norm for many early abolitionists. It'd be rare to find an early abolitionist who believed that the two races were completely equal. But, as Bordewich semi implies, Jefferson indeed may of gotten more racist over time, partially due to frustration. Jefferson often spoke, and acted, towards getting rid of slavery. Certainly his reflection of the failings to rid of slavery in 1784 show how frustrated he was about the his own failings, and the failings of the country as a whole to get of rid an institution that he so much despised.

Hope that helps somewhat. I'm hoping someone more knowledgable than me can comment.