Interestingly, when the Civil War started, Robert E. Lee was offered the command of the Union forces, but after his home state, Virginia, seceded, he resigned from the U.S. Army and joined with the Confederates. Many people wonder why Lee would turn down the command of the Union forces and support the Confederacy. But loyalty was one of Lee’s bedrock traits and he couldn’t wage war against Virginia and the South. Also, recent historians are presenting a more balanced view of the long festering and complex events leading to the Civil War. (An example being inequitable tariffs – the South paid 87% of the nation’s total tariffs in 1860 alone.) The new research contained in these books puts a new light on Lee’s decision to fight for the South.
I suspect that another reason Lee decided to support the South was President Lincoln’s refusal to meet with Southern representatives to try to reach a compromise to avoid war. Although members of Lincoln’s own cabinet as well as newspapers in America and Europe encouraged the President to attempt a negotiated settlement, he remained adamant. Lincoln rejected all requests for discussions that might have led to a peaceful resolution.
Robert E. Lee vigorously opposed slavery and as early as 1856 made this statement: "There are few, I believe, in this enlightened age, who will not acknowledge that slavery as an institution is a moral and political evil." Lee also knew that the use of slaves was coming to an end. Cyrus McCormick’s 1831 invention of the mule-drawn mechanical reaper sounded the death knell for the use of slave labor. Before the Civil War began, 250,000 slaves had already been freed.
Robert E. Lee did not own slaves, but many Union generals did. When his father-in-law died, Lee took over the management of the plantation his wife had inherited and immediately began freeing the slaves. By the time Lincoln issued the Emancipation Proclamation in 1863, every slave in Lee’s charge had been freed. Notably, some Union generals didn’t free their slaves until the ratification of the Fourteenth Amendment in 1868.
http://www.lewrockwell.com/orig/jarvis10.html
The tariffs were not inequitable. Tariff rates were uniform and legal as the Constitution provided. Such well used complaints from apologists for the Confederacy reminds one of the whining by the antebellum pro-slavery loudmouths that they would be discriminated against if they couldn't take their slave "property" into the territories. No discrimination there-Yankees couldn't take slave property into the territories either! :)