The whole area of Jefferson and his stance on slavery is hotly debated (and given Jefferson's role in the founding of America one that can rile people up) so I'm going to try not to be too controversial here.
Jefferson was indeed quite forceful in his words regarding slavery in Notes on the State of Virginia, however his stance in that text isn't exactly rooted in concern for the African-American people who were enslaved. Rather he is concerned with the potential for moral corruption of white people - not because they owned slaves in of itself, but because he was concerned about white slave owners being unable to stop themselves from abusing their slaves and thereby teaching the next generation to solve their problems through violence, he mentions the "degrading submissions" inflicted on the slaves but it's clearly not the main thrust of his concern:
There must doubtless be an unhappy influence on the manners of our people produced by the existence of slavery among us. The whole commerce between master and slave is a perpetual exercise of the most boisterous passions, the most unremitting despotism on the one part, and degrading submissions on the other. Our children see this, and learn to imitate it; for man is an imitative animal. This quality is the germ of all education in him. From his cradle to his grave he is learning to do what he sees others do. If a parent could find no motive either in his philanthropy or his self-love, for restraining the intemperance of passion towards his slave, it should always be a sufficient one that his child is present. But generally it is not sufficient. The parent storms, the child looks on, catches the lineaments of wrath, puts on the same airs in the circle of smaller slaves, gives a loose to the worst of passions, and thus nursed, educated, and daily exercised in tyranny, cannot but be stamped by it with odious peculiarities.
While you can't exactly view it through modern eyes Jefferson's opinions of black people weren't exactly geared towards racial equality - he believed black people to be inferior in their intelligence, beauty and ability to form deep emotional bonds.
While he didn't seem to express any particular hatred of black people, and conversely is reputed to have treated his slaves relatively well. He just didn't consider them the equal of white people.
The notion of simply abolishing slavery and freeing the black peoples in America didn't sit well with him - he feared that doing so would only result in a never-ending racial war, from "Query XIV":
It will probably be asked, Why not retain and incorporate the blacks into the state, and thus save the expense of supplying, by importation of white settlers, the vacancies they will leave? Deep rooted prejudices entertained by the whites; ten thousand recollections, by the blacks, of the injuries they have sustained; new provocations; the real distinctions which nature has made; and many other circumstances, will divide us into parties, and produce convulsions which will probably never end but in the extermination of the one or the other race.
Instead his proposal was that current slaves should remain so and their children should be repatriated en-masse to Africa.
Jefferson certainly took political actions against slavery (such as signing the Act Prohibiting Importation of Slaves of 1807 into law and while his political rhetoric around the time was largely general denunciations of slavery his responses to political/legal drives towards freeing slaves already in the country would tie more with the concerns he outlines in Query XIV above.
Regardless of what his personal feelings on the manumission of slaves may or may not have been there remained a certain amount of pragmatic reality to his continued slave ownership and resistance to that being changed - put simply he couldn't afford it. His building efforts at Monticello in particular had left him significantly in debt, losing the substantial slave labor he had inherited (he was the second largest slave owner in Virginia IIRC) would almost certainly have bankrupted him and it is likely the economic drive that caused him to only support anti-slavery initiatives and proposals that would preserve the economic value he received from the 100+ slaves he owned.
So basically, while it was likely that Jefferson was strongly against slavery in concept, he had strong motivations based on both fear of reprisals from mass-freed slaves and his own precarious economic position to at least limit himself to the actions aimed at preventing slavery going forward. So he wasn't a mustache-twirling evil slaver - he was just trying to balance the realities of an imperfect world and do the best he could.