Yes, the FreeTaxUSA software will prepare your Minnesota M1PR return (Property Tax Refund) when you are going through the Minnesota section of the software.
The Form M1PR is a separate tax return from your regular Minnesota tax return. You can still e-file your regular Minnesota return.
FreeTaxUSA doesn't charge an extra fee for the preparation of the M1PR return. It's included when you buy your regular Minnesota tax return.