Why do I have to pay more tax on my 1099-R if I already paid the tax when I took it out?

The federal income taxes withheld on the 1099-R is only an estimate based on the gross distribution.

The taxable amount of the distribution is entered on your tax return as ordinary income and taxed at your current tax rate.  The federal taxes withheld are entered on your tax return as a tax payment.

If your total tax liability is less than your total tax payments you will receive a tax refund for the overpayment.