As I understand it, the current situation is this: raw materials sell for their full purchase price, while crafted items sell for 50% of their purchase price. 

Raw materials include things like food (including cooked food, like fish cakes and meat soup), cloth (even the crafted kinds, like magic cloth or ethereal cloth), the various woods (including ancient wood), and mined materials (from stone and iron to obsidian and adamantine); crafted items are things like outfits, tools, weapons, and potions (including beer and whiskey).

By itself, that isn't a problem; I've been assuming that raw materials are basically commodities in this market, things traded at full value as though they were themselves alternate forms of currency. The problem comes in when the value of crafted items is consistently less than 200% of the value of the necessary materials to craft them. 

This means that if I have, for example, 10 Mythril and 8 Obsidian, I can either craft a Master Mythril Staff from it (value: 1035 gold), which takes at least one turn of a skilled craftsperson's time to make, and then sell that product for 517.5 gold... or I can just sell the 10 Mythril and 8 Obsidian at market (total value: 910 gold), which takes no time at all, and make 910 gold.

Where is the value of my craftsmanship?

My suggestion is this: either reduce the sale price of raw materials to something less than 100% of value, increase the sale price of crafted products to something greater than 50%, or both. As things stand, it feels like a waste of a class to have someone become a Blacksmith only to learn that it's more profitable to simply sell the output of our mines directly.

Same with grain/bread at game beginning. 

For me, the value of the blacksmith is in making tools, weapons and other items that make other workers more efficient. If you really want your blacksmith to earn money directly, you can have them make steel. I don't think it would be a good idea to rebalance the game so that crafted items make a profit, since it would be really easy to wreck the balance of the game. 

There's also nothing a skilled craftsman can make that an unskilled craftsman couldn't. It's not even any more difficult for an unskilled craftsman to make a valuable item than a skilled one, they just generate generic "work units" slower.

Food is also an interesting subject. Obviously you've only got 4 types: vegetables and grains which are the cheaper options, and meat and fish which are 50% more expensive. Vegetables and meat are the "rarest," which means there's "only" ~50 units of each at the neighboring town, bread is the most plentiful with ~100 units of grain and ~50 units of bread, and fish would be in the same boat as meat and veg except you have a resource node unlocked at the beginning of the game. Therefore, I think it makes sense that making meat soup is the most profitable use of your chef's time, while bread is the least.

There are items for each crafting station that sell for more than you can sell the ingredients for. Most items don't, but they are there.

Dagothurmum, I'm aware that changing the sale price of crafted items relative to the sale price of raw materials would change the balance of the game. However, I would be equally happy with a reduction in the sale price of raw materials (without changing their purchase price) as I would be with an increase of sale price of crafted goods (relative to their purchase price). Since the former would make the game harder and the latter would make the game easier, surely a balance could be struck that would make gold however difficult or easy to obtain as the designer likes?

It's also interesting that you bring up that the only difference between a skilled craftsman and an unskilled one is how long an item takes to make, because this is exactly why I feel that crafted items need to make a profit in order to justify the existence of the crafting classes. Consider: if I'm only crafting items to equip my own household, then I only need to make a small number of items before I'm set for life. There are only a few people I need to equip for a few different things, and once they have their gear, it will never wear out. Whether a particular set of tools takes three turns to craft or six is unlikely to matter at all -- after acquiring the materials needed to make gear to my standards, the actual crafting is an afterthought. What crafting classes do by speeding up the crafting process is multiply the income generated by crafting.

If my blacksmith generates income by crafting steel but costs me money when he crafts a steel sword... why are people selling swords at market? How is that netting the sword vendor a profit? Do all steels swords on the market come from dungeons? Do the members of the Worker's Guild pick them off of sword bushes? If there's a government crafting subsidy reimbursing craftsmen for artificially keeping the prices of crafted goods down, where is the paperwork I can fill out to get me some of that?