First of all, I am no accoutant but I have too much experience paying taxes.
If you made $3K on a job of net profit, then depending on your tax bracket, which being a small business means somewhere in the range of 30-40% of net profit, you would have a tax bill of $900 to $1200 for this project - kinda sucks doesn't it.
This is where you need an accountant to be sure you get the tax deductions you deserve. Equipment depreciation, insurance, workers comp., office expenses, phone, etc,etc are all deductions that need to be itemized because you are spending this for business and you for darn sure don't need to be taxed on these items. The senario you described is gross profit not net profit. All of the above mentioned items and several more, are deducted from your gross profit to determine your taxable (net) profit.
Hope this helps.