Even our flat rate shipping is based on weight. There is no way around that. To charge flat rate shipping, rather than entering cost, all you are entering is weight for the product or packaging and then using your custom price per ounce, which essentially provides you a much more flexible system of charging a flat rate for each item or multiple quantities of each item.
To charge a flat rate for the whole order, just set weight to 0 for everything and enter a handling cost in Shipping settings.
For an example please see http://www.e-junkie.com/bb/topic/1149