When your tax preparer tells you she will be there to help you in case of an audit, she doesn't actually come to help you unless the IRS actually calls you into an office for a one-on-one meeting. In that case, your tax preparer must be there. However, if the audit is conducted via mail, there is no obligation on the part of the preparer to come to your place of residence because the audit is conducted via mail - which is how most IRS audits are conducted.
Now when you spoke to her asking if everything was claimed correctly, she told you YES and in her eyes, it was. However, in the case of the IRS, they will scrutinize everything much more closely to the point where you will pay more. The $5,500 you have to pay is not because she did a poor job, but because the IRS determined that you underpaid taxes based on deductions she took on your behalf that the IRS just happened to disallow. The problem here is that if she had done the tax return exactly the way the IRS wanted the return to be done - you would still owe the $5,500. It was not a penalty you were assessed; you were assessed for unpaid taxes.
As a traveling nurse, you're an independent contractor. As such, your returns will more than likely raise a red flag with the IRS and the risk of an audit is always going to be high. If the $5,500 were penalties that were assessed and she didn't pay them, then you might have a point. But from your description, that isn't the case...