"General Lee" is General Robert E. Lee, commander of the Confederate Army of Northern Virginia. The entire story takes place against the backdrop of the Civil War, and Lee was one of the most prominent figures in that conflict, leading the main body of the Confederate Army in Virginia from 1862 to the war's end in 1865. Johnny Dutton's decision to resign his commission in the United States Army when the war breaks out in 1861 is paralleled by Lee's decision to do exactly the same. Lee had been offered command of the Union Army charged with crushing the rebellion, but chose to resign rather than to fight against Virginia. Johnny's admiration for him shows that he was famous throughout the South, and is also a device for Walker to introduce an interesting piece of trivia about the Confederate leader, as well as to portray Southern confidence at the war's outset:
He's the man that got that crazy John Brown, the one they hanged for treason at Harper's Ferry in Virginia...The South is bound to win under his leadership, and I mean soon!
Lee had, in fact, become famous as the commander of the U.S. Army detachment that apprehended John Brown after his seizure of the federal arsenal at Harper's Ferry. He is one of several historical figures that is referenced in the novel. Lee would go on to become, despite his defeat, widely regarded as a military genius and venerated as a hero throughout the South.