Prices are determined by the economic principle of supply and demand. There is greater demand to fly from Atlanta (ATL) to Japan (JP) than many other nearby random cities in the southeastern United States. This demand is intensified by the fact that ATL is a hub for Delta Airlines (DL), which creates a reluctance by DL to lower prices, given the fact that people will pay more for a nonstop.

Fares are not based on distance or cost, except in a most general sense. Obviously, if they are losing money on a given route over the long term, and airline may have to raise fares or reduce (or eliminate) service.