Yglesias has some good points on this (bolding in original):

Two points on this. One is that in 1860 about 60 percent of the human beings in Virginia were slaves and thus neither leaders nor soldiers nor citizens of the Confederacy. Why should Virginians neglect to think of them? Surely slavery was a significant part of the conflict for the 30 percent of Virginians who were slaves and did, in fact, welcome the advancing Union soldiers as liberators. Allow me to quote from Jay Winik’s April 1865:

As white Richmond retreated behind shutters and blinds, black Richmond spontaneously took to the streets. From the moment Union troops entered the city – ‘Richmond at last!’ Black Union cavalrymen shouted – crowds, the skilled and the unskilled, household servants and household cooks, rented maids and hired millworkers, jammed the sidewalks to catch a glimpse of the spectacle. No longer enslaved, they thrust out their hands to be shaken or presented the soldiers with offerings: gifts of fruit, flowers, even jugs of whiskey. Federal officers riding alongside promptly reached for the liquor bottles and smashed them with their swords. But the crowd was undaunted. Just a day earlier, they had been prohibited from smoking, publicly swearing, carrying canes, purchasing weapons, or procuring ‘ardent spirits.’ Yet now, to the sounds of ‘John Brown’s Body,’ they jubilantly waved makeshift rag banners; to the tune of the ‘Battle Hymn of the Republic,’ they enthusiastically hugged and kissed the bluecoats.

Slavery obviously seemed significant to the slaves. And, of course, it was significant to the architects of rebellion as well. Here’s the first paragraph of Virginia’s ordinance of secession:

The people of Virginia in their ratification of the Constitution of the United States of America, adopted by them in convention on the twenty-fifth day of June, in the year of our Lord one thousand seven hundred and eighty-eight, having declared that the powers granted under said Constitition were derived from the people of the United States and might be resumed whensoever the same should be perverted to their injury and oppression, and the Federal Government having perverted said powers not only to the injury of the people of Virginia, but to the oppression of the Southern slave-holding States:

And there you go. Of course a long and bloody war has a number of aspects, but this was primarily a conflict around the issue of slavery.