When you are using the CD/Download desktop software, 1 free download of the state software to prepare your state return is included but there is an e-file fee for the state returns. You can avoid that fee if you print and mail the state return instead. You can print and mail as many of that state return as you'd like. But if you choose to e-file it, you are charged a fee. See here Is there a fee to e-file my state taxes?
If you go here TurboTax CD/Download software and then click on "1 state download" under the Home & Business version, it will provide this information for you as well and show "E-file additional" and the current e-file fee is also shown there if you scroll to the very bottom of that pop-up window.
And as for the $39.99, that is the fee that Refund Processing Services charges when you opt to pay your TurboTax fees from your federal refund. You can remove that option and pay your TurboTax fees with a credit/debit card in order to avoid that fee. That fee does not go to Intuit, the federal government or your state. It goes to the bank that handles the refund processing.
More on the Refund Processing service can be found here What is the Refund Processing Service? and here Who provides the Refund Processing Service?
