Someone wrote a nice comment on a YouTube video of the song:

hi, someone from Coal Country, Pennsylvania, here. i live and breathe coal. many of the men in my family were miners or worked in the mines. coal is a big part of my family’s short history here. when he says, “I owe my soul to the company store,” he is being quite literal. the way the coal companies were set up was they would pay their workers in credits—basically coupons only redeemable in their stores, the company stores. they could not be traded in for American dollars. additionally, many people that worked in the mines also lived in houses built and owned by the coal companies. they were small, narrow, and only the bare minimum were put into the homes (stove, bed, etc.). the companies would take so much out of their wage to cover housing costs that they could barely afford to exchange their credits in for the basic necessities in the company stores. many of the workers and their families fell into deep debt. what’s better (sarcasm) is that when a worker died or was injured in the mines, the living family would not receive compensation from the company that owned said mine. many had to rely on fellow workers and their families just to get by, much more so if there was a death or injury in a family. so yeah, many miners did essentially owe their souls to the company stores.