A "run" in this sense is "everything a manufacturing process produces". It's also used in phrases like "run of the mine". It means total output regardless of quality , shape or size. So to ask for or buy "the run of the mill" means you're happy to take everything they've got, good, bad or indifferent - you'll find a use for it. So to describe someone or something as "run of the mill" means average/ not special.