Lee was against slavery because he thought it was bad... for white people. He felt slavery was a great deal for black people, actually. Read this excerpt form a [1856 letter Lee wrote]:(https://www.theatlantic.com/national/archive/2010/08/arlington-bobby-lee-and-the-peculiar-institution/61428/)

I think it however a greater evil to the white man than to the black race, & while my feelings are strongly enlisted in behalf of the latter, my sympathies are more strong for the former. The blacks are immeasurably better off here than in Africa, morally, socially & physically. The painful discipline they are undergoing, is necessary for their instruction as a race, & I hope will prepare & lead them to better things. How long their subjugation may be necessary is known & ordered by a wise Merciful Providence. Their emancipation will sooner result from the mild & melting influence of Christianity, than the storms & tempests of fiery Controversy.

It’s an ugly sentiment. Lincoln meanwhile was against slavery because it was cruel. This is a very very different view than Lee’s.

Furthermore not only was Lee and slave owner, and a nasty one at that. He inherited salves from his father in law. They were the descendants of George Washington’s slaves:

As executor of Custis’s last will, Robert E. Lee was charged with freeing the bondsmen within five years. Yet some of the enslaved insisted they were to be freed upon their master’s death, causing a conflict with Lee that resulted in a failed escape attempt from Arlington plantation by three of the enslaved. Under Lee's order to “lay it on well,” each of the rebels endured up to 50 lashes and suffered excruciating pain as the wounds were bathed in brine. Lee also broke with Custis and Washington family tradition, separating most of the enslaved families under his control.

I can not imagine Lincoln ordering slaves whipped and salt rubbed in their wounds.