National cemeteries are for dead US soldiers. Confederate soldiers do not get buried in US National Cemeteries. Neither do German or Japanese WWII veterans, or Viet Cong, or North Koreans, or Saddam Hussein's Republican Guards.

To answer the other part of your comment, why would you think the Confederates were not "laid to rest with the respect like the other soldiers"? They were buried by their friends and comrades, among their fellow Confederate soldiers. I can think of no greater honor.