I'd do a flat base rate roughly equivalent to fuel, gonz and one respawn, plus a scaling base rate per jump (scaling by safety, per jump), and a "penalty fee" for doing shit that makes us more likely to get shot at.
Let's toss some numbers. Say we're making a five-jump trip; two jumps are through poor-security space, one jump is actively in enemy territory, and the hauler is hauling a very small load of very high profit margin items (a pirate's ideal target goods, earning him the Penalty Fee). The cost would be:
1x Flat Fee......................||1x 1500cr.....1500cr
1x Penalty Fee................||1x 500cr.........500cr
2x Safe Jump Rate.........||2x 250cr.........500cr
2x Low Sec Rate............||2x 500cr.......1000cr
1x Enemy Space Rate....||1x 750cr.......1500cr
Total:.....................................................
4250cr
EDIT: I am inordinately upset that the