Yep I saw huge losses some weeks too when I had the economic setting on medium.
I now play on low, as the huge losses didn't make sense to me.
I liked the idea of raw materials availability, and it certainly made me think about what enterprise to open in different towns. I had a very varied port-folio when I tried that
The huge losses come about as the enterprise manager decides to source the raw materials elsewhere when they are not available, even though the finished product will be sold a close to the standard cost. If the enterprise were to not produce anything that week, so that losses were limited to the wage/upkeep part, then it would make more sense to me.
I did try to source the raw materials myself for a while too, but I ended up closing most of the enterprises down in the end.
My brewery in Dhirim did OK though, AFAIR.
To answer your question, you'll still be able to find enterprises that turn a regular profit in most of the towns.
Go through the entire list before automatically deciding on building a dyeworks everywhere. Let it run for a few weeks and be prepared to go back and close it to build something else if there are too many lossy weeks.