While one of the requirements of being a working owner of a corporation (subchapter S or C) is that you take a salary, it is generally understood (even by the IRS) that a new company may not have enough income to pay the owner initially.
Since this is the first 1120-S that you have filed, the fact the you are not yet taking a salary in a company that is not showing a profit does not increase your risk of being audited. TurboTax automatically generates the "Audit risk alert" any time that no shareholder salary is inputted into a subchapter S corporation return.
