One way to address the problem is to acknowledge there will be differences. Regular freight (i.e. containerized types) will basically have a flat rate per container/dton. Bulk items, like grain and such will receive the lowest rates since they are relatively time insensitive. High tech, luxury or high value goods would receive a premium. Goods that are hazardous might also receive a higher premium since they are dangerous (radioactives, corrosive gases). So a price chart might look like:
Bulk goods: -10% price from standard
Standard: no discount or premium
Premium: +10% from standard
Other things to consider would be how much babysitting the cargo requires. For example, transporting a small herd of quadrapeds from one system to the next could require a premium since live animals need more care and handling. Delivery not to the main port but a smaller, out of the way port, might be a reason to charge more since it's less likely to find another cargo at a smaller world than the main system starport. Also, a rush job such as an immediate pickup and delivery could require a surcharge. Reference tables are great since both players and referee's can consult them to get a understanding of what to expect. Plus they are even more greater for a lazy ref to fall back on when they are busy fleshing out other parts of their gaming universe and don't want to have to deal with this.
Passengers would be treated the same way, with the exception that there needs to be even more variance. To go along with this there needs to be more variables related to cabins as well. Steerage in the future is essentially 4 people in one room - but it's far more comfortable than what steerage used to be in the 1900s. Along with that are the different types of cabins that the rich will pay big credits for. The most expensive suites on a ship are pretty damn big, and the charge for them is just as big. However the game has only ever postulated the same size room for every ship. That's not at all realistic, especially now that we see airliners with apartments on board them, let alone what ships have had in the way of cabins over the last 150 years. Size will vary, depending on the need and use, but costs need to be standardized for designs:
Basic stateroom – Cr75,000/ton. They are basic and functional. Applicable for low passage, military bunkrooms, prison transport. Depending on the purpose, the number of personnel that may be included per room varies (i.e. low or military transports may house 1 per dton, while prison transports may house 2 per dton in more cramped accommodations. Life support would be sufficient and livable, though not terribly pleasant.
Standard stateroom – Cr125,000/ton. The ‘standard’ for Traveller staterooms. Suitable for crew, middle passage transport.
Luxurious – Cr175,000/ton. Suitable for officers, 1st class passengers, standard for low end yachts, corporate transports or poor nobles.
Opulent – Cr250,000/ton. Suitable for high end yachts, rich nobles, flag rank officers, high-end corporate transports, very wealthy.
Somewhere I've got a chart showing costs per transit. I'm still waffling on whether to make it per parsec, or per jump. The goal is to keep it simple, but also recognize both costs and profit margin.