PayPal gets a cut but not Ebay. There is no way for ebay to levy fees on shipping charges.
eBay charges against "final value." From the eBay fee FAQ:
"Final value fee
If the item sells, you're charged a final value fee. Final value fees are calculated based on the total amount of the sale and are charged per item.
The total amount of the sale is the final price of the item, shipping charges, and any other amounts you may charge the buyer. Sales tax is not included."
http://pages.ebay.com/help/sell/fees.html