Either way you look at it.. you are still paying an additional $39. Either from your card or from your refund.

No.  If you pay the 39.99 by credit card you avoid the 39.99 Refund Processing Service charge (44.99 in California)  but you have to go back and remove it the right way.

There is no charge to get Direct Deposit.  

That is for a state return or probably the extra 39.99 Refund Processing Service charge.  You can pay with a credit card to avoid the extra charge.

Deluxe is 39.99
State is also a separate 39.99 in all versions above the Free Edition
If you select to have the fees deducted from your refund there is an EXTRA 39.99 Refund Processing Service charge (44.99 for California)

So you could have 2 charges of 39.99 for 79.98 (or 84.98 for Calif)
Or you could have 3 charges of 39.99 for 119.97 (124.97 Calif)

How to see your fees
https://ttlc.intuit.com/questions/2565973-how-do-i-review-my-fees-in-turbotax-online

For help with fees
https://ttlc.intuit.com/questions/1901213-what-can-i-do-to-reduce-my-fees

How to remove the Pay from your Refund fee
https://ttlc.intuit.com/questions/1900517-how-do-i-remove-refund-processing-fees-in-turbotax-online-...

YES you are being charged another $39.99 and TurboTax does NOT want you to know that.   FREE E-File on TirboTax is NOT FREE anymore.

I already paid $39 for the software at Amazon

I paid the $39.99 already when I bought the software on Amazon

Assuming you are trying to determine why you need to pay when e-filing your returns, the fee you paid for the software may not have included the electronic filing  fees for your state.  This may be why you are being asked to pay when you try to electronically file your return.

 

(The sample below shows the prices for downloads online at the moment.  If you notice, the federal e-file is included but it is an additional fee to e-file the state returns depending upon the product you purchase.)

 

Downloading TurboTax Desktop versions