My wife is an Amazon seller and yes when she ships prime she must pay for shipping which would force her to lose money on each shipment so she builds the cost of shipping into the cost of the item. The cost of her taxes are in the item. The cost of her employees are in her item. The cost of software licenses are built into the item.
The only thing you get with FREE shipping is a receipt that doesn't include shipping as a line item. Someone has to pay the driver, buy the truck, and put fuel in it, pay for the insurance, etc, etc, etc. It can't possibly be free.