The root cause is a constant reward regardless of distance. IMO the only way to fix it properly is to scale traderoute income with distance * cargo.
The reason you want to use distance rather then time is because this gives an advantage to fast new designs. In reality a shorter traveltime would rather cost an extra premium, not the other way around.
I thought about distance instead of time or fuel as well, but aside from being surely more difficult to determine in a system where civils already are
the calculation hog nr.1 already, I dismissed the idea because distance is an illusionary since relative price factor.
I see it like this: 200 years ago, shipping some nice clothes or sweets that you wanted from US to Europe would have cost a lot, and they would still arrive slowly. Shipping technology advanced beyond the sail eventually, and transportation cost went down.(of course as secondary factor also due to tighter logistic networks) However, we can of course still get a fast delivery for more money (like airmail), but is that really because of technology advance? No, not really, still more or less same fossil ovens, yet it costs more because of the less efficient transportation (fuel/energy expense per weight unit) or having to act outside of established supply lines.(personal taxi at 10 is more expensive than 9 O'clock train)
If technology were to advance to give us say personal around-the-world jet/vtol drone delivery with a cheap as hell He3 fusion motor, transportation cost would not go up, but instead shrink even further. In an eventual extreme, a star trek transporter system would probably cost you a stamp mark worth of electricity in the end.(..and this is true even if we had it between planets and stars)
So the point is that, yes, within the realm of your
current technology level faster transportation will cost extra, as a faster "ship" or whatever will use less efficient engines, or you need to charter(or build in aurora) a special clipper for an outside of routine job.
Space and distance are relative though, and if your means to get around become more efficient (and at the same time sometimes faster), the expenses of shipping fall down as well, so as long as there is competition on the market, that will push providers to attract with lower prices eventually, if not immediately.( as a "sell-point" of the new technology for example. the flyPhone! faster than your old hauler and microwave oven combined, and can be located via galactic-positioning-system at all times!)
Faster transportation technology virtually 'shrinks' the world around you, and with that all kind of things happen:
1 - highest possible delay of ware supply decreasing (mitigating the "readiness" price component of rare wares)
2 - better reaction time ensures that business can make more secure deals (reducing the "risk" price component. Risk is not really pirates, but actually more inherent long term investment danger since long delays between request and delivery might mean you will be beaten to it. What you do is usually you factor in some sort of self insurance each time, - otherwise you are just gambling on your luck.)
3 - if it is also more fuel efficient, you might actually save on energy, which is probably the base factor to the whole transport cost equation
? - ...possibly more things I can't think of right now
So in some cases the 3rd point's price increase (less efficient engine) might override the advantage of the two speed advantages, which creates these fast "taxis" that might be situationally useful at some point, but wont evolutionary survive on the mainstream market.
An advance in technology is therefore made if that doesn't happen, so if you get at least a price of d1+d2+d3<0, you have found a cheaper way to do it despite being faster.
...Which means the economic returns of transportation tax go down as technology advances.
...Consequently also meaning that time and fuel are the actual influencing factors, as distance is only a influence, but what really counts is how fast+cheap you can cross it.
