In the first few chapters sales will be rather accidental even if you furnish the rooms with (relatively) good equipment, and put decent sales people in. Notice that the standard clerk is a bit of a joke as well. That is not to say you should not bother with furnishing the workshop though. There should be relatively decent options available for every room, that you have acquired in the process of clearing maps and finishing quests.When does the shop start actually making sales? I've had stuff listed there and gone on half a dozen adventures since then but nothing ever sells out of it. Got furniture set up that should be helping. Is the rando shopkeeper really that bad? I'm having a really hard time making any money because of this. Come back to town and just more taxes and no income.
The best way to make money in the early game is to avoid buying stuff as much as possible. Only spend money on quests (like Kokahuren's drinks) and on expanding your workshop. Don't bother with buying potions and such - money is quite tight, and if you play well, you won't really need them anyway. Clear every map 100% as well (which will give you a once-off every map).
There is also the option of going to Deadbeat Dungeon to make money through collecting the treasures there. Don't even try to beat the Deadbeat King (lv 70 map), it will be useful later in the game. Those treasures can be sold at the church.
Also, if you do simple maps, you could leave one or two NPCs behind to boost sales a little bit (preferably characters with high Service ratings), since you won't need them anyway. Not sure where you are (I am guessing chapter 4 or 5), but you could also look at easy things you can synthesise through Alchemy that will sell for a bit of coin, with ingredients that are easy to collect. For example the Pumpkin Ornament, Gorgeous Bookshelves, are fairly good items to mass produce and make money that way. Harvesting the required materials should be relatively straightforward.