Well for one, I don't hate anyone with the flag, but I often do prejudge them to be a bit ignorant. Not saying I'm right, but I have yet to meet someone that is so hung up on it that isn't racist. Not saying they aren't out there; but I haven't met them yet and they are definitely in the minority.
And like I said, I don't see a lot of sense in clinging to a failed symbol of rebellion, esp. when the rebellion was for a crappy cause. Up until that point, the american flag represented who they were as much as anyone else in the americas and after they lost it did the same. It represented the south only at a time during the war and what they were standing for at the time. To try to change it into some sort of symbol of southern pride because they don't like having lost is a reach.
If I didn't grow up there, I'd probably have a hard time understanding it too. It has absolutely nothing to do with having lost the Civil War though. It's not even controversial in Mississippi, except when some outside group comes down and tries to tell people how they should
feel about it.