When you choose to have your fees paid from your federal refund, there is a $40 processing fee to use that service. The fee is assessed whether your fees are actually paid from your federal refund or if TurboTax must get the fees directly from you when your refund is late.
The reason it is still assessed is because your refund will still go to the 3rd party bank that was going to take your fees out when the IRS finally sends it and they must then handle it to send it on to your bank.
See the FAQ referenced in Volvogirl's answer.
