That is why subsidized merchants exist. Governments basically guarantee the loan.
You are also assuming that Jump-1 is acceptable. If the stars are a bit sparser, Jump-1 ships might not fill the bill. The Egryn Subsector of the Leviathan adventure would not work for Jump-1 ships at all.
The problem is that at LBB2 cargo rates (Cr1K/ton/Jump) and stated operations tempo (1 Jump per 2 weeks), the only ship that can cover its costs for Jump-2 is TL-15 and has a 3439Td cargo bay (out of 5KTd) -- which under the trade mini-game, it can't possibly fill. Nothing smaller can, nor can any of a higher Jn.
In regions such as Egryn/Trojan Reach, this means that either there is no market for transport of freight except within the clusters of adjacent worlds, or freight rates are higher than Cr1000/ton/Jump. However, the rules do not provide for this possibility.
The thing about Subsidized Whatevers is that they set a
ceiling on freight costs where they operate. A shipper can find ships that would haul freight for less than Cr1000/ton profitably (even a Type A Free Trader can!), but no ship can find a shipper willing to pay more than Cr1000/ton because shippers can wait for a subsidized freighter.
And while there's a de jure rate of Cr1000/ton/jump, there won't be many ships willing to eat the losses (let alone financed and built in the expectation of doing so) of taking that rate on jumps above Jump-1. So, in practice, freight costs would eventually approximate Cr1000/ton/parsec, though there is no mechanism in the rules to support breaking up a freight shipment into multiple J-1 legs.
This is a case of the rules not only not matching the setting, but also not even matching their own implications.
The setting description implies that there are indeed shippers that pay more than Cr1000/ton/jump (if only as internal bookkeeping), but for some reason these shippers will never contract with the player characters for shipping except by referee fiat.
(Again, LBB5 may produce ships that could do J-2 at less than Cr1000/payload ton/Jump (2), but I haven't checked yet.)