While large restaurant chains can take advantage of their scale to get supply chain discounts and squeeze out smaller competitors with lower prices, small chains can also use their scale to get more discounts. But smaller restaurants tend to have the edge in terms of profit margins, given the same operating conditions. That's because they have a greater cost advantage. Small stores are run by couples or partnerships between friends who are both owners and waiters, and people don't make money through dead wages. When you own a business, the first thing you want to do is to lower your payroll costs to make sure the store can operate longer. Costs such as benefits and insurance are reduced or even erased accordingly. The biggest cost is probably just the cost of three meals.
Additionally, a small husband-and-wife store can extend its hours with the logic of "if we don't sell out today, we're going to waste it," or even maximize profits by spanning the hours of operation from breakfast to late-night snacks. But in a chain, it's hard to extend hours for something like this. If chains need hundreds of customers a day, then perhaps a couple dozen can feed a small store. This allows them to reach deeper into neighborhoods, into areas where chain restaurants are afraid to go, or are relatively hesitant to go.