Joseph Wheeler, Jr., son of Gen. Joe Wheeler who commanded the cavalry of the Army of Tennessee, etc., graduated West Point in 1895.
Simon Bolivar Buckner, Jr., son of Gen. S.B. Buckner, who surrendered Ft. Donelson to Grant, and commanded a corps under Bragg at Chickamauga, etc., graduated with the West Point class of 1908. He was killed in action at the battle of Okinawa in 1945, and later posthumously awarded a fourth star by Congress.
Here's the supposed last photo of Gen. Buckner (at right), taken just before he was killed by a fragment from a shell:
Besides generals' sons, there were many graduates who were sons of Confederate Veterans. General Mason Matthews Patrick, who commanded the US Army air service during World War I, and was instrumental in developing the US Army Air Corps in the '20s, was the son of a Confederate army surgeon.
Admiral Hilary P. Jones, who after WWI was commander of the US Fleet, was an 1884 Naval Academy graduate, and son of the commander of the artillery of the Second Corps, Army of Northern Virginia at Gettysburg...
Admiral Husband Kimmell, who commanded at Pearl Harbor during the attack in December, 1941, was a Naval Academy graduate, and son of a Confederate Army major.