So, in the TU that I'm working on, ships are cheap, jump drives
aren't. I gave every component except jump drives a 75% discount (I
really wanted my cheap small craft so I can have space RVs), while
jump drives are at 150% book cost.
Now, the issue with this is that with the freight and passenger income
as written (especially with the assumptions that Mongoose writes
in...), there's no need to adventure except as an accident (I know
I'll take a safely profitable milk run any day over having to do shady
stuff to make ends meet... And where's the adventure in that?). And I
don't want that. I assume that making a profit off shipping and
passenger runs, with no speculative trade, is for companies dedicated
to building a consistent shipping run between two worlds. Such
companies can swing subsidies for runs light on cargo and passengers.
PCs will need to seek out speculative trade and patrons (and solve
problems for patrons who might give them a cargo...) in order to pull
a profit.

But, I want to see what other people think of my numbers and methods
(all items built with Mongoose 2e).
I started off with a 400-ton subsidized merchant, modified to carry a
triple turret and 1 ton of sandcasters. I assume a 20% subsidy, 65% of
cargo is freight, 1 container of mail, 50% passenger capacity (with 1
high passenger), and it makes 25 jumps a year (assuming a 2week
lay-over when the techs go real deep on the maintenance). Crew is
double bunked (and base salaried). Fuel is purchased unrefined (fuel
processors).
I calculated all costs of just running the ship and converted them to
the per jump amount, arriving at cr125,685
The per run costs for passengers was also easily done: 4 low berths
occupied, 8 staterooms occupied, 8 rooms unoccupied. All base LS costs
(the cr1000/month) already included in base per jump costs. 1 high
(extra cost: cr1000), 14 mid, double bunked (extra cost cr14000), 4
low (extra cost cr400). Costs are per month, so they were converted to
per jump: cr7392.
Freight is 128tons, mail is 5tons.
Total costs per jump: cr133,077
Net tonnage in use: 167tons
Now we subsidize: 20% gives us an operating cost of cr106,462/jump
costs per ton: cr638

Now, here comes the interesting bit: I decided to run the numbers on a
basis of freight being cr500/ton. Mail is 5x that per ton. Passengers
pay per jump LS costs (total cost per person), plus tonnage cost for
their stateroom (or portion of). Passengers got rounded up.
So I ended up with (for one parsec)
Freight: cr500/ton
Mail: cr12500/packet
Low: cr300
Mid: cr2750
High: cr3500
running it on the example ship gave some pretty heft differences with
subsidy: profit with was cr13,738/jump. No subsidy left the ship
almost cr13,000 in debt.

So then I ran a Type A, max capacity (no high passengers, double
bunked mid, no mail), and the crew on shares: cr415 short (over 10K
short across the entire year). With a single mail packet, profit of
cr9,585 per jump. If the crew was salaried, it would be 415 short
again.
Suppose it's adventuring time, eh? Or should I adjust my numbers,
considering just how easy interstellar trade is IMTU? Or is the
assumption of subsidy fine?