Those parking lots are not owned by the stores. It's usually by the city or some other property investor. If it happens to be a store-owned parking that charge

Those parking lots are not owned by the stores. It's usually by the city or some other property investor. If it happens to be a store-owned parking that charges per hour, it's to prevent abuse from drivers going to other stores nearby if it's in downtown. Charging for parking outside your store in a less dense district is equal to putting up a sign that you don't want customers.