By default when shipping a package, the Rates tab shows both what each shipping option costs you and what you're charging. If customers can see your register screen, go to Settings → Business → Rate Display and turn off or hide the cost display. If you hide it, it will still be visible but disguised to look like an unintelligible random number, like a product code, but it's actually the shipping cost in pennies.
Customers will still see the sale prices, and so will the customer-facing display if you have one. Your cost remains available in reports.