Do I have to pay a fee for withdrawing money from a Roll over IRA?

Withdrawals from a traditional (pre-tax) IRA are always subject to regular income tax, plus a 10% penalty if you are under age 59-1/2 (unless an exception applies).  You will get credit for the $2050 of withholding, but the tax could be substantially more than that depending on your age, other income, and other circumstances.  $12,000 total taxes ($2000 withholding plus a $10,000 change on your return) is not unreasonable depending on your age and other income. 

Yes, depending on if this was an early withdrawal, you would have a 10% penalty on the $41k along with your regular tax rate on your other income.

As you walk through the questions after entering your 1099-R, TurboTax will say "Lets see if we can reduce this penalty"  Here is will ask you about Penalty Exceptions that may reduce or eliminate the penalty you received. 

In the meantime, if you are unable to pay your taxes in full, you should still file by April 18th, but you can apply for a payment plan from the IRS.  When you get to the end of TurboTax, prior to hitting file, it will give you the option to apply.