Add Handling Fee To Flat Rate Shipping Method

add-handing-fee.php

function wc_ninja_change_flat_rates_cost( $rates, $package ) {
	// Make sure flat rate is available
	if ( isset( $rates['flat_rate'] ) ) {
		// Adds a $3 handling fee to the existing flat rate shipping method.
		$rates['flat_rate']->cost += 3; 
	}

	return $rates;
}

add_filter( 'woocommerce_package_rates', 'wc_ninja_change_flat_rates_cost', 10, 2 );