How do I get the direct deposit fee removed from total when I've decided to pay the filing fees with a credit card?

There is not a fee to e-file your tax return or to have direct deposit of your refund.

Did you choose to pay for using TurboTax by having the fee taken out of your federal refund?  That means you will pay an EXTRA FEE of $40 ($45 in CA) to have a third party bank receive your refund from the IRS, take out enough to pay TT, and then send you the rest of the refund.  ( The third party bank keeps the $40 or $45 fee for itself.)

You do not have to do that.   Pay upfront BEFORE you file --- pay using a credit or debit card.

REMOVE REFUND PROCESSING FEE

https://ttlc.intuit.com/turbotax-support/en-us/help-article/intuit-account-billing/remove-pay-refund-fees-turbotax-online-change/L7UxC6ZZp_US_en_US?uid=m6r4xelq

There is not a direct deposit fee using TurboTax. 

What you are referring to is the Refund Processing Fee by the third party processor when you requested to have your TurboTax account fees paid from the federal tax refund.

See this TurboTax support FAQ for removing the pay with refund fee - https://ttlc.intuit.com/turbotax-support/en-us/help-article/intuit-account-billing/remove-pay-refund-fees-turbotax-online-change/L7UxC6ZZp_US_en_US?uid=m9irnvm6

I'm not sure what fee you are referring too.

You can review your fees by following the instructions below.   

• After signing in to TurboTax, open or continue your return. 
• Select Tax Tools on the left side of the screen and then Tools. 
• A Tools Center box will pop up on your screen. 
• Select the My Fees box on the right. 

If your TurboTax fees are higher than expected, you can reduce them by removing add-ons: 

• Remove PLUS Help & Support 
• Remove Pay With Your Refund 
• Remove Premium Services 
• Remove MAX Defend & Restore 
• Remove a state