The Form 1099-R you entered has a taxable income to be reported on the federal tax return. The federal taxes withheld in box 4 of the form are a tax payment, just like the federal taxes withheld on a W-2 are a tax payment. You did not pay the taxes on the withdrawal, you had taxes withheld.
If your total tax payments are greater than your total tax lability then you will receive a tax refund for the overpayment.
If your total tax payments are less than your total tax liability then you will have taxes owed on the federal tax return.