The entire system is currently pretty strange. Even family farms wind up feeding into corporate wholesale conglomerates. So the "small farms" that are non economic wind up supplying the corporations who pasteurize, package, process, and market the milk for retail both as milk and as other finished products. The corporations that can bear the regulatory and other costs wind up profiting from the farmers who are indentured to the government. They may not be literally indentured but it's a good metaphor for the relationship. They get bottom price milk from subsidized producers while keeping the retail profits.
Grocery stores have tons and tons of loss leaders. Anything perishable unless it is premium priced is probably going to lose money. Dealing with low priced perishable, refrigerated, fragile, leaky products is really tough. The profits are in dry goods, drugs, supplements, and prepared foods.