You have to indicate in TurboTax that your withdrawal is from contributions by entering your Prior Years' Roth IRA contributions.
In TurboTax Online, after you have entered your form 1099-R, TurboTax will take you back to the summary page titled Your 1099-R Entries.
On that page, click Continue and follow the TurboTax interview until you arrive at the page titled Enter Prior Year Roth IRA Contributions where you can enter the amount of your past contributions.
If your withdrawal is less than your past contributions, there will be no tax or penalty.