I don't think its the pay that is different at low cost airlines, I think its more the hours worked - most pilots work to the legal maximum.
If you look back through aviation history, in the past there have been periods of pilot shortages and pilot surpluses. During the times of pilot shortages, the pilots can ask for better pay and conditions, and because airlines are having trouble recruiting enough people, the pay and conditions generally improve. Then there starts to be a pilot surplus and the companies start to claw back on the pay and conditions. Typical "supply and demand" problem I suppose.
At the moment we have just gone through a pilot surplus due to the effects of Sept 11th. However, we are now looking towards a pilot shortage, I believe, for a number of reasons - low cost airlines heavy recruiting for expansion plans; BA, Virgin, Emirates and Qatar recruiting; charter airlines recruiting; after Sep 11th a lot of potential pilots chose not to train, so there is a bit of a gap.
This will be countered by the opening up of Europe, with new countries joining, and pay here being better than many of the new EU countries.
The main change to airline pilots has been in terms of working hours, not pay.