Required reading for the angered:
The Confederates wanted to split the nation into two, primarily to keep the majority of southern black Americans enslaved. The flag itself didn't regain popularity until the anti-segregation movement of the 1950s and '60s. This was when the South was still Democrat. The Democratic party at the national level began to oppose segregation. This led to the short rise of the Dixiecrats, who re-popularized the Confederate flag. Then during the Presidential election of 1964, Democrat Lyndon B. Johnson supported the passing of the Civil Rights Act while Republican Barry Goldwater voted against it. This began the South's transition from Democrat to Republican. This is why people call the Confederate flag racist, it was created to keep black Americans enslaved and it regained popularity to deny them equal rights.
Note: I was both born and raised in the South, so don't mistake this for "Northern bias".