Although both rockets have roughly equivalent upmass, their respective delivery vehicles are completely different beasts: Dragon is a compact spacecraft, design

Although both rockets have roughly equivalent upmass, their respective delivery vehicles are completely different beasts: Dragon is a compact spacecraft, designed to safely fly humans in a shirtsleeve environment and return them to Earth, whereas Cygnus is more like a large pressurised can with some thrusters attached. Cygnus has no downmass capability at all, but has a LOT more pressurised volume -- and in some cases (including, possibly, the recent SpaceX launches to the station), volume rather than weight can be the limiting factor for payloads. It's not implausible that NASA used some kind of formula which prioritised volume over weight, and arrived at the respective payments for each type of mission. Of course neither is it implausible that Orbital Sciences simply has better lobbyists than SpaceX.