I can't comment too much on Jefferson's wider moral and political philosophy because I'm someone who studies slavery in comparative contexts rather than the history of the United States itself, but I wrote an answer to a follow-up in this thread a few months ago that a lot of people seemed to find really helpful in getting their head around how Jefferson could reconcile his slave ownership with his political philosophy emphasising freedom and self-determination. It's a very long answer that runs to the character limit so I can't reproduce it in quote form below, I'm afraid. One key takeaway I would say to be aware of is that Jefferson is by no means unusual of slave owners in his life time, it's just that his particular historical significance as an individual and lasting impact of his political ideas in American political culture that makes him seem somehow uniquely problematic and hypocritical as a figure.
Hey there. This is incredibly similar to this question which I answered not long ago: How could american founding fathers fight for freedom of all men and allow slavery?
So I will copy and paste this answer here. If you have any follow up questions, please let me know!
This is a great question, one that has been debated by historians for decades, but I'll try and explain some of the over-arching themes.
Context So I like to try and explain a few things right from the very beginning. In 1776, the year the declaration was penned and endorsed, slavery existed in the north as well as the south. The first state to ban slavery was Vermont, in their 1777 constitution (but this state was so new and so small that hardly any slaves existed and thus were freed). Next, in 1780, Pennsylvania passed a law saying that the Children of slaves would be free once those children reached 28 -- but this freed no slaves immediately because children born in 1780 would have to wait until 1808 for their freedom. Massachusetts' Supreme Court ended slavery in 1781 when two slaves sued for their freedom (and won). And while this appears to be rather radical, it was rather slow. By 1810, there were still 30,000 slaves in the North because several still allowed slavery past this time period (Slavery was abolished by these states in these years: Maine 1820, NY: 1827, NJ: 1846, CT: 1848).
So why bring all this up? Because we often times believe that slavery was a Southern issue that barely, if at all, affected the North and this is a complete fantasy. It became a northern issue, but at the time of the Revolution, many in the north were not keen on freeing slaves. Let me be clear though, unlike the South, the North's economy did not rely on slavery to thrive, so it was a more pressing issue for the South than the North because of this.
But also keep in mind, that it was the invention and adoption of the cotton jin in the 1790s that made slavery skyrocket in the south, therefore greatly increasing their need for more slaves. So just be aware that the way Americans viewed slavery in the 1770s was very different than how they would view it decades later.
Answer Slave owners, who were mainly the gentry since slaves were expensive to buy and even more costly to pay for their food, clothing etc. over time, saw slavery as a necessary evil. The blatant hatred for African Americans and slaves that we see in pop-culture hits featuring the 1800s or Civil War era hadn't quite hit yet. This was still a period of the enlightenment, so the Founding Father's claimed that their actions for keeping people enslaved were justified for one reason or another. What did they say themselves, well, let's look at their words together:
George Mason of Virginia, who owned hundreds of slaves.:
"Slavery discourages arts and manufacturers. The poor despise labor when preformed by slaves. Every master of slaves is born a petty tyrant. They bring the judgment of heaven on a country."
I can only say that there is not a man living who wishes more sincerely than I do, to see a plan adopted for the abolition of [slavery]—but there is only one proper and effectual mode by which it can be accomplished, & that is by Legislative authority: and this, as far as my suffrage will go, shall never be wanting.
But when slaves who are happy & content to remain with their present masters, are tampered with & seduced to leave them; when masters are taken at unawar[e]s by these practices; when a conduct of this sort begets discontent on one side and resentment on the other, & when it happens to fall on a man whose purse will not measure with that of the Society, & he looses his property for want of means to defend it—it is oppression in the latter case, & not humanity in any; because it introduces more evils than it can cure."
As you can see here, both of these men, who owned many hundreds of slaves together, speak very harshly of slavery. Even more noticeable is that Washington says he would be in favor of the abolition of slavery himself if it can work its way through the necessary legal means to do so -- which he knows is nearly impossible. And this is sort of at the heart of the answer to your question. There is a paradox here, where slave owners (for the most part) seem to recognize that slavery is a bad thing, yet they seem unwilling to take any steps to fix it.
I would also be remiss if I did not talk about the reasonings of some slave owners who advocated to keep slavery because they believed that it was a benefit to the slaves themselves. It is likely shocking that Jefferson (who is known as one of the most revolutionary minds of the era) was one of these people. Again, let's pull up some of his own words.
Folks like Jefferson will often give multiple reasons why they believe slavery should not be abolished. First, is their own self preservation. He believed that if slaves were granted freedom, they would likely revolt and kill the one's who once owned them. Here, take a look:
Ten thousand recollections, by the blacks, of the injuries they have sustained; new provocations; will… produce convulsions which will probably never end but in the extermination of the one or the other race.
But as it is, we have the wolf by the ears, and we can neither hold him, nor safely let him go. Justice is tin one scale and self preservation in the other.
There is a very real sense of fear here, one that, in Jefferson's mind justifies the existence of slavery at at time where white Americans are fighting for their own freedom.
The other reason is, in my opinion, a much darker one. It's one where African-Americans who are enslaved are then said that they are north worthy of freedom because they are either unintelligent or somehow inferior to whites. Again, here are Jefferson's own words:
But the slaves of which Homer speaks were whites. Notwithstanding these considerations which must weaken their respect for the laws of property, we find among them numerous instances of the most rigid integrity, and as many as among their better instructed masters, of benevolence, gratitude, and unshaken fidelity. -- The opinion, that [black slaves] are inferior in the faculties of reason and imagination, must be hazarded with great diffidence... the blacks, whether originally a distinct race, or made distinct by time and circumstances, are inferior to the whites in the endowments both of body and mind... I think one could scarcely be found capable of tracing and comprehending the investigations of Euclid; and that in imagination they are dull, tasteless, and anomalous.
So what does all this show? Well, it shows that the very man who penned the Declaration of Independence believed that enslaved people would kill their masters if freed and that they were physically inferior to white people. There are other reasons I could dive into, but these really are he most pressing ones that he founders typically gave. This is the real start among southerners to start justifying slavery due to differences in race, and it is something that will escalate throughout the 19th century.
I just want to add a thought: Is it possible that slave-ownership, in a lot of respects, is not, necessarily, different from being an Employer? What I mean is: if you respect the human rights of your slaves--if you treat them with kindness and compassion, feed them, clothe them, and care for them--are you really treating the man as less than an equal?
I realize this is a History question, not a philosophical one, but this idea has been nagging at me for a long time. I really believe that the dark, tainted word "Slavery" inherently discolors the discussion. Without knowing what kind of Owner Jefferson was, I think it's patently unfair to assume that him owning slaves was an obvious, inalienably contradiction to his belief in Human Rights.