I think the flight supplement comparisons done above is a little difficult to compare, as others have mentioned.
Tour operators base their basic prices for a package usually from a "London Airport", and not necessarily Gatwick...
Gatwick usually has far more frequencies of charter flights to the popular destination likes of Tenerife, Faro, Palma, etc... Maybe flying 4-6 times a week and only once or twice a week from Luton.
The NIL supplement flights will usually be based on the most anti-social flights to the destination, which are going to be the least popular. For example a flight to Palma departing a London Airport at around 10-11pm and flying back from Palma at 3am.
Due to the shear number of flights and frequencies from Gatwick these flights are more likely to be from there.
I thought I would look up a holiday at random (identical for three departure airports) for a family of 4 staying on the same dates and identical hotel and same airline, I discovered the following prices:
STN- £2832.00
LGW- £2580.00
LTN- £2412.00
Did you check other flights from Gatwick for the same week to the same destination and hotel? As they may have had a flight to this destination on another day with an even lower supplement from Gatwick than the Luton option.