– It was on a major railroad line.

– There was a strong contingent of Confederate women in the area who raised money to have NC soldiers removed from battleground graves (mostly in VA and PA) and reburied in their home state.

If a family was wealthy enough, they might send someone with a wagon to travel many miles to return the body of a fallen son after learning of his death. Unfortunately, few were able to do so.

The post-war reburial movement was quite active in the decade following the CW, as was the movement to honor the dead with monuments. It was strongly felt that Confederate dead should be buried in their native soil, and that they should be honored with statues and markers.

Most Southern towns had some sort of women’s organization that participated in these efforts.
These ladies would take up “subscriptions” for funds to recover the bodies of fallen soldiers, often removing them from battlefield graves or temporary cemeteries in other states. In many cases, the bodies were removed from the temporary graves and sent to Richmond for identification (where possible) and then further removal to the soldier’s home state.

The railroads made much of this possible, and most of the larger Confederate cemeteries are to be found in cities that were served by existing rail lines.

John — Another reason Raleigh buried so many Civil War dead is because there were several wartime hospitals here — most notably Pettigrew Hospital. The Confederate Cemetery was established in 1867 in order to accommodate the removal of bodies from the hospital site, which had been appropriated by the Federal authorities for the burial of Union soldiers (now known as the National, aka Federal, Cemetery).
http://www.raleighpublicrecord.org/featured/2009/02/15/raleighs-confederate-cemetery/

Side note: Arlington National Cemetery was literally built in Robert E. Lee’s front yard. The Supreme Court ordered Congress to pay his heirs $150,000 for improperly taking the land.