In addition to needing to stock them, shops need to level before they generate any useful amount of money. Don't expect to open one and have it be anything but a money hole for a while. If you want to make money, shops are good given time and the ability to keep them stocked, but performing might be more accessible (though a bit of a grind) in the early game, and once you have the skill it's probably faster, more reliable and easier to do performance quests for gold than pretty much anythig else.
In any case, I'd recommend not worrying about gold for a while. Platinum is far more valuable. Do quests, level up your skills, become more powerful. Trade cure corruption potions or stacks of oracle scrolls to adventurer's to get gear. There aren't many things you need gold for: real estate deeds and potions of potential, mostly. Those are definitely very useful, but it's sort of a long term endeavor to set up a castle and level up vendors to farm potions from.
If you're at a stage of the game where setting foot in the puppy cave is even something that would occur to you, seriously...don't worry about gold. You don't need it yet. Do quests for platinum and level your skills more.