The game is unbalanced, especially in the early 1800s. Maybe it's just too easy to raise big bucks and build inter-city long lines decades before they emerged in real life. Still, you can make money on freight if the distance is short and the locomotive is cheap.
Income shifts somewhat in the "2nd century", and then pax & mail dry up in the 1960s after the announcement of air travel.
In my US History map, I gave certain freights some added value: You can reduce the costs of building rails by producing lumber and steel. I created some fuel cost triggers as well.
And yes, I separate freight depots from passenger terminals in all but my lowest-traffic towns. It's also a good idea to keep slow freights on their own tracks where they won't be frozen out by a steady stream of express trains overrunning them. Carefully placed diagonal crossings can allow a network of freight lines to be completely isolated from an overlapping net of express lines.