That flag was introduced in 1862 because the traitor national flag looked so much like the US flag that it caused friendly fire incidents. I agree that flag does not represent the politics of the war, it was issued to the field army's of the south only. The flag can be seen as racist when it is taken out of it's context of course, as can any other flag, so where do you draw the line.
The ugly truth is that the Civil War was not fought over slavery, but over a political system and economy that the South increasingly became more paranoid of and viewed as against hostile to their interests and survival, who do you think bought and became rich off of the cotton by manufacturing it? The Northern states and the Great Britain. 75% of the 5 million spindles in America were in the Northern states.
During the New York City draft riots freed slaves were murdered on sight by Irish immigrants and hung from street lamps all over the city.
Times were totally different, Woman were considered property at this time as well.
It was also a poor man's war, if you owned 10 slaves or more you were exempt from service in the traitor Army, and in the North you could pay a tax to evade service as well.
The South saw this war as a second revolution , Robert E. Lee's father served under George Washington as his Cavalry commander and his wife was directly related to George Washington and many other traitor's were related to the founding fathers of old.
The emancipation of slavery was not the cause of the war, but a result of the war, but the traitor flag and monuments sure make great political punching bags to keep people's eyes off of the US flag and the monuments to the founding fathers.