Getting rid of your cargo from pax a/c is almost always a bad idea. Here’s why:
The only direct cost (as far as I am aware) for taking cargo on a passenger flight is “Cargo Handling” under “Variable Costs” on the flights finance page. For example, on one of my 727 flights with full cargo I can fit in 16CU with full pax load. The pure revenue from this cargo is AS$1,754, the Cargo Handling cost is AS$400. Therefore the CM I profit is AS$1,358. This total is the real profit/loss from taking the cargo on that particular flight, therefore it is clearly worth taking the cargo.
Because Cargo Handling costs scale with the amount of cargo carried, there are very few reasons or situations where you want to reject all cargo. After all, it only fills cargo if there is spare capacity in terms of max take-off weight.
While it may seem cargo is making a loss, this is only because all other costs such as Fuel, Landing Fees, Maintenance etc are spread across both passengers and cargo in the Flight Costings page, in a way that loads more costs against the Cargo column. In other words, these costs are the same no matter whether you have loaded the cargo or not (except perhaps some extra fuel, because of the extra load?).
Hope that makes sense?
TLDR - It’s almost always worth taking the cargo with any spare capacity.