In the FAQ, there is a section entitled "The Civil War and Slavery". There are two excellent answers by /u/Borimi, among other ones. I'll put here some of the more succinct points, although it obviously would be better to read both of the posts (and others in the thread) in their entirety.

Essentially, the war started over disunion: The South wanted to dissolve the Union and the North was willing to fight to preserve it. The war was caused by slavery. Essentially all the differences which were large enough to affect the conflict were rooted in the relative presence or absence of slavery: the social differences, the economic interests, the states' rights argument, the political interests, everything. But more than that, both the North and the South were fighting over their interpretation of the legacy of the Constitution and the Founding Fathers. Each society had a different perspective on what principles the country was founded upon, and when the war broke out both sides believed they were protecting the legacy of the American Revolution. This is why the Civil War is sometimes referred to as the Second American Revolution.

I've heard it best described, in simple terms, by a panel of historians a couple years ago: "while slavery and its various and multifaceted discontents were the primary cause of disunion, it was disunion itself that sparked the war." (source)