It's a different story if the material value of the metal in the coin exceeds its face value - at that point it makes sense to go to a bank, change money into pennies, then scrap them and sell the copper. That would be bad.
But the reason pennies are a bad deal isn't because of their manufacturing cost, it's because their handling costs exceed the value of incorporating them in a transaction. Should a store go to the trouble of keeping pennies available, counting them, storing them, transferring them to the bank? Or should they round up change to the nearest five cents and take a 4c hit on each transaction where you'd have been able to use pennies? If your average transaction value is over a hundred dollars or so, like most supermarkets, and you only handle cash on one sale in 50 say, if handling pennies in your cash-management operation takes more than a few thousandths of one percent of your budget, it's costing you too much.