Hi,
I’ve replied personally, but in case if anyone else has similar question, I’m posting same here:
I think what you need to do is go to your fee’s settings (e.g. “WooCommerce > Settings > Payment Gateway Based Fees and Discounts > Direct bank transfer”) and there (at the bottom of the settings page) there is “Product Categories – Calculation type options” – please try changing that from “For all cart” to “Only for selected products”.
Hope that helps.
Best regards,
Tom