This is a very complex subject which unfortunately like most subjects taught in U.S. education is done simplistically and superficially. My thoughts:
Prior to the emancipation proclamation, the "north" and more specifically the Federal government had absolutely no intention of changing the status of Negroes. The war began because of the "southern" perspective that their agrarian culture (which used slave labor) was to be wiped out by the industrialized culture of the "north". The war was about state v. federal rights.
From "Why America Failed: The Roots of Imperial Decline" by Morris Berman
"Most Northerners believed, at least initially, that the war was not about slavery as a moral issue. In an address to a special session of Congress on July 4, 1861, Lincoln stated, “I have no purpose, directly or indirectly, to interfere with slavery in the United States where it exists”, repeating what he had said at his inauguration earlier in the year. Secession, he said, was the real issue, for the Union must be preserved at all costs (the Union Congress passed resolutions endorsing all of this). Lincoln already made it clear that he did not favor social and political equality for blacks “in any way” and was a major proponent of repatriating them to a colony in Central America. For other Republicans, moral opposition to slavery was a non-issue."
The Confederate battle flag and all other representations have now come to be solely identified with "the peculiar institution" -- slavery. Initially, it did not represent only that issue.
Perhaps the greatest mistake Lincoln made was not allowing the southern states to secede. Is this not one of the tenets of democracy that people are allowed to determine in what way and under what organization they wish to live? Where is it written that the U.S.A. as it existed then and now will continue, or should for that matter?
Lastly, I would suggest that the U.S. flag currently represents to many around the planet economic and military subjugation, and death and destruction. And, no, not all those who feel this way are "Muslim" or "Arab".