Why? Because at the time when Abraham Lincoln was president of the United States, most of the Confederate soldiers who were fighting during the Civil War hated Lincoln and wanted him dead.
In fact, the man who assassinated Lincoln on April 14, 1865 -- John Wilkes Booth -- was a racist who was supported by other people who were in the Confederate army. Booth also was a Confederate sympathizer. Booth, Confederate sympathizers and many other people who were in the Confederate army were strongly opposed to the abolition of slavery in the United States, and Lincoln's proposal to extend voting rights to recently emancipated slaves.
Booth and a group of co-conspirators also had led a plan to kill Vice President Andrew Johnson and Secretary of State William Seward in a desperate bid to help the Confederate cause. This may have been one of the main reasons why the Ku Klux Klan supported the Confederacy and its rebel flag.
This is according to some information I saw online and in some books about the Civil War in the public library. There also are some movies and documentaries about the Civil War -- for example, The Civil War (1990), produced by Ken Burns, is a very accurate documentary about the Civil War and the assassination of Lincoln.