BAA Charges
The reason for the hike in prices is very simple.
For more years than I care to remember, BAA was allowed to cross subsidise it's airports with the result that charges at Stansted were held artificially low as revenue from Heathrow and Gatwick was used to offset any losses. Luton Airport certainly tried to get this arrangement stopped on many occasions even resorting to complaining to Brussels.
BAA's ability to cross subsidise is no longer allowed by the CAA - in other words each of BAA's airports has to stand on its own feet. Thus in the case of Stansted were income has been less than costs, the only option has been to increase charges.
In addition, I would guess that in some cases, the special deals available to all airlines when setting up routes to new destinations are coming to an end - I think they typically expire after two or three years.