... They are also paying more property taxes (more than the local guy because his land area is much smaller and in a cheaper part of the city). Their sales, which are probably larger volume overall, are producing tax revenue for the county. Besides which, I live here and support the local economy by shelling out a fortune in property taxes, sales taxes, motor vehicle taxes, parking taxes, etc...
Don't forget to factor the incentives that municipalities give to large box stores to come into their area. Heaven forbid a large company open a store in an area without seeking various tax incentives, etc, they all try to negotiate favorable term and will threaten to build elsewhere if they don't get the incentives. So while their tax base is still larger than a mom and pop, it didn't come without some costs.