Why did the Declaration of Independence raise questions about slavery?

The Declaration of Independence raised questions about slavery because of its assertion that "all men are created equal," and that they are entitled by virtue of being human to basic, natural rights. Obviously, this runs counter to the very idea of slavery, which is the ownership of human beings by other human beings. Of course, eighteenth-century assumptions about race prevented many from fully grasping this contradiction at the time, but many Americans, in the wake of the Revolution, did free their slaves, motivated by the rhetoric of equality and rights that was so much a part of the age. This was especially true in the middle and northern states, where slavery was very much on the decline by the late eighteenth century. Even in the South, many slaveowners (most famously George Washington) freed slaves in their wills. But the institution of slavery survived in the South, and was given new life by the emergence of short-staple cotton as a cash crop after the development of the cotton gin. Interestingly, a very direct and uncompromising critique of slavery included in the original draft of the Declaration was removed at the insistence of delegates from South Carolina and Georgia. It placed the blame for the slave trade squarely at the feet of King George, and is worth quoting here at length:

he has waged cruel war against human nature itself, violating it’s most sacred rights of life & liberty in the persons of a distant people who never offended him, captivating & carrying them into slavery in another hemisphere, or to incur miserable death in their transportation thither. this piratical warfare, the opprobrium of infidel powers, is the warfare of the CHRISTIAN king of Great Britain. determined to keep open a market where MEN should be bought & sold, he has prostituted his negative for suppressing every legislative attempt to prohibit or to restrain this execrable commerce: and that this assemblage of horrors might want no fact of distinguished die, he is now exciting those very people to rise in arms among us, and to purchase that liberty of which he has deprived them, by murdering the people upon whom he also obtruded them; thus paying off former crimes committed against the liberties of one people, with crimes which he urges them to commit against the lives of another.

If included, this remarkable indictment of the slave trade and slavery itself would have added a powerful antislavery element to the document, which is exactly why delegates from the Deep South demanded that it be excised. But clearly, the signers of the Declaration, including Thomas Jefferson, the slaveholding Virginian who produced it, were thinking about the contradictions between liberty and slavery.