If TurboTax is telling you that you need to pay $1,000 it would be because you earned money and didn't make quarterly payments so you have taxable income and a tax liability that has not been met yet.
For people who work for someone else as an employee, the employer withholds the taxes from their pay every check. If you are a business owner, you are responsible for making your own payments to the IRS. In addition to the normal taxes that you would need to pay, you are also liable for self-employment taxes.
Self-Employment taxes are your Medicare and Social Security taxes. They are 15.3% of your profit.
The $59 you paid is for the software to prepare your return. TurboTax, nor any other tax preparer can keep you from paying any taxes if you have a tax liability.
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