local airport Surcharges

Just wondered if anyone could explain why the likes of Vigin and TCX etc always charge extra to fly from regional airports such as Manchester, even on Long haul routes? when you look at things like flight tracker the Virgin Gatwick-Vegas flight takes a northerly route passing east of MCR, if the MCR-Vegas flight takes the same route it would be using 200 miles less fuel each leg!!!!, and as the airlines base planes at regional airports there is no extra required for repositioning? explanations please