Rocket fuel is RP-1, a highly refined form of kerosene, & an oxidizer - usually liquid oxygen.
Stratolaunch doesn't need an oxidizer.
In 2011 Elon Musk said fuel for the first stage of a Falcon 9 cost about $200,000.
Stratolaunch/747s burn a somewhat different (from RP-1) type of kerosene known as Jet A, though when it's cold they burn Jet B for its enhanced cold-weather performance.
Right now at Mojave Air and Spaceport, which is where Scaled Composites is based, Jet A is $4.57 a gallon.
Falcon 9 has 9 rocket engines that burn fuel at a very much higher rate than the 6 jet engines Stratolaunch has.
According to the Wikipedia page, a Falcon 9 Full Thrust mission (allowing booster recovery) was about $62 million in 2016 - new first stage booster.
Missions using recycled first stages cost less. I don't know how much less because it's more recently Space X has used recycled first stages.
So the question boils down to - How many Stratolaunch missions does it take to cover the cost of building, operating, and storing the aircraft.
Obviously, Scaled Composites believes they'll be able to make a profit.