They do make a profit. A plastic bag does not cost 20-45p to make. Instead of the business providing the bags complimentarily, instead of the customer paying for the cost of the old plastic bag, the businesses are selling a slightly nicer plastic bag for profit.
The reason they weren’t priced from the beginning is because plastic bags are ridiculously cheap, so they could afford to do it as a complimentary item. The reason they introduced them was to get people to shop more, as people would buy less when they didn’t have bags. So the business could write off the cost of cheap bags for the extra profit from increased sales.
Then, after a few decades’ conditioning, the businesses have taken what was complimentary and started charging a marked up price for it. People now know that it’s better for them to shop with bags, so businesses are taking advantage of that, all while pretending that they’re “doing the green thing”.