I agree that the freight system is bit weird but I have had some success at setting up line-haul freight trains- I set up a main trunk line served by frequent mixed freight trains (carriages for all commodities) with truck routes or branch lines feeding each industry to a local freight station on the trunk line.
In my current game, I run the trunk line completely across the entire map with enough trains to maintain a 2-minute frequency. The trains are barely profitable, but when you combine them with the feeder routes, the whole freight system makes good profits. I found that a small number of industries quickly expanded to full production (400 units) but most others chug along (10-25 units) and the result is that trains are full for some parts of the route, empty for some parts and most of the time run with small load of all commodities.
However, the big plus that I found with this model is that every city along the route receives goods and so grows- which makes the passenger service more profitable.
I’ve also made this model work using a central freight yard and running multiple trunk line from it to the different regions on the map. Its the only way that I have found so far to create a destination for goods that can take hundreds of units at a time (a requirement if you want to run long freight trains).