You aren't being taxed twice. You didn't actually pay the tax when you got the payment. You had an amount withheld from the payment to be applied towards the total tax on your tax return. The amount that was withheld is a down payment towards your total tax for the year.
The amount that was withheld from the payment should be in box 4 of the 1099-R. When you enter that in TurboTax it will be applied towards your total tax. It will be included on Form 1040 line 25b as a payment that you already made.
