I mean, it's a nice addon, but does it make sense to add "cargo delivering missions" for a public transport like a subway? It's not the same thing as a cargo train.
Blame R* for their logic. As said, you can play this side mission while driving passenger trains in GTA: SA (see this if you somehow don't believe it) and I added it to LC for the sake of consistency.
just fix that logic by replacing the text "Cargo" with the text "Passengers", do you agree to do that?