Add the following to your theme's functions.php to show product documents only for logged in users. Note that this is a very simple example, and could be expanded upon to show documents only for a particular user role, only for particular products, anything! http://www.woothemes.com/products/product-documents/

wc-product-documents-document-access.php

<?php

add_filter( 'wc_product_documents_get_sections', 'show_documents_only_for_logged_in_users', 10, 3 );

/**
 * Don't return document sections unless there is a logged in user.
 *
 * @param array $sections array of sections
 * @param WC_Product_Documents_Collection $collection the collection object
 * @param boolean $include_empty whether to include empty sections in the result
 * @return array sections for display
 */
function show_documents_only_for_logged_in_users( $sections, $collection, $include_empty ) {

	// this check can be made as specific (by user role, etc) as desired
	if ( ! get_current_user_id() ) {
		return array();
	}

	return $sections;
}