This snippet will add a 5% surcharge to the customer’s cart, but you can change the 0.05 value as desired.
// ADD SURCHARGE % TO ALL WOOCOMMERCE ORDERS
add_action( 'woocommerce_cart_calculate_fees','woocommerce_custom_surcharge' );
function woocommerce_custom_surcharge() {
global $woocommerce;
if ( is_admin() && ! defined( 'DOING_AJAX' ) )
return;
$percentage = 0.05;
$surcharge = ( $woocommerce->cart->cart_contents_total + $woocommerce->cart->shipping_total ) * $percentage;
$woocommerce->cart->add_fee( 'Surcharge', $surcharge, true, '' );
}