I'm not aware of any rules in any of the books about the cost of fuel for the ship (maybe vague verbiage, but nothing concrete).
Then it occurred to me, maybe the GM could set a base cost for travel and have it be altered by the Astrogation roll (higher/lower cost of fuel due to efficient path take)? Normally I'm a hard RAW guy, but this house rule is appealing to me. It wouldn't be a separate Astrogation roll, it would just be a part of the same roll that takes you to the destination system.