It's not being taxed twice. What is happening is, you are paying self-employment tax (FICA: Medicare and Social Security tax) because you were issued a 1099 and not a W-2. When you have a typical W-2 job, the employer will take care of the withholding, as well as pay for 1/2 of the payroll tax.
Bonuses are wages that are subject to federal income tax, state income tax, and FICA taxes. Although you're not technically self-employed, the self-employment entry in TurboTax allows you to enter the income, and then calculates all the appropriate tax on this income.
