TT is not charging you anything ... the feds & states require that you pay your taxes during the year as you earn the income just like you do on a paycheck. If you will owe a $1000 or more on your tax return (even if you pay it in full timely) you are subject to an under withholding penalty which is calculated automatically.
You might be able to eliminate it or at least reduce it. You can go to Federal Taxes tab or Personal tab, under Other Tax Situations and select Start by the Underpayment Penalties. You will answer a series of questions that may reduce or eliminate the penalty. Or you can elect to have the IRS figure the penalty for you. It's form 2210.
Federal Taxes or Personal (for H&B version)
Other Tax Situations
Additional Tax Payments
Underpayment Penalties - Click the Start or update button