It is entirely consistent to oppose slavery (a gross violation of human liberty) while still supporting secession (the breaking up of governments—which themselves constitute a gross violation of human liberty.) As the confederate flag has historically been used as a symbol of both these ideas (along with being a more generic symbol of heritage and history), it is also understandable how those who oppose one idea while supporting the other may be conflicted on the issue.
I can certainly understand why some people are less than thrilled with a symbol which has been used in some cases to advance and promote an agenda of racism and slavery, but I also understand why those who view the symbol as an important reminder of resistance to tyranny are none too happy with the latest efforts to purge the symbol from public use.
In this case, as in all cases, I choose to view the issue through the lens of personal liberty and free speech. Yes, the symbol may be disturbing to some, but so could a belt or a hairbrush if such items were wielded by an abusive parent. The crimes of the past cannot be allowed to demonize or disallow the use of objects or symbols which also have other meanings or uses.
The real question should be what the current user of a symbol or image is attempting to convey rather than how the symbol may have been misused in the past. If someone is obviously using the confederate flag to promote a racist agenda (by carrying it in a KKK march, for example), it is appropriate to condemn that usage of the symbol, but if the usage is more ambiguous (such as a bumper sticker on a pickup), it is most appropriate to either assume the best or seek out the truth. Many people who choose to display the confederate flag are doing so for reasons other than racism.
There are some who want to give up on the confederate flag and 'throw the baby out with the bathwater' as it were. Its history is too tainted, they say, but if this logic is followed, what comes next? The Christian cross was used as the symbol of the crusades and is still used by certain white supremacist groups. Should that symbol be universally rejected as irredeemably offensive? Some of those in the Black Panther movement are radical nationalists. Should black panthers (the animal or the comic book character) be eschewed?
Giving up on the confederate flag will be seen—rightly or wrongly—as giving up on secession, and that would be a very unfortunate outcome. Even though the motives behind the secession of southern states prior to the War of Northern Aggression were not all pure, the principle of secession is still critically important to anyone who wants to break the stranglehold of empires over individuals. What do you think the original American War for Independence was if not an act of secession?
For me, the use of the confederate flag offers an opportunity to talk about the evils of government and the important principle of secession. Others may prefer a different strategy. For those who choose to take offense at the use of the confederate flag—even when no such offense is intended—I say that's your right, but it's not really a logical decision.