there can be many many reasons but usually its one of 3
Overbooking at the commercial planning stage, these are the airline teams who decide how many and who to sell these seats to, be it the Tour Operator, direct or 3rd Party. These are planned maybe a year in advance but often the aircraft will change so for example a CFU flight that was planned on a Boeing 757 with 235 seats but for a myriad of reasons was later changed to an Airbus A320 with 180 seats, causing 55 passengers to overspill.
Consolidation. For prices to remain competitive aircraft need to be full, a situation even worse now with the fuel prices. If there are 2 half full Corfu flights going from Manchester within a reasonable time of each other then they might be merged. Be grateful if you fly charter to Corfu if this was scheduled chances are it would be just be cancelled. One thing travellers never seem to made fully aware of is that flight times are not and never will be guaranteed, its on your ticket, hidden on the back in the conditions small print, conditions you agree to when purchasing the ticket. Good piece of advice, more so these days always read what you are agreeing to.
Slots. Aircraft can not just roll down the runway and take off whenever they want, slots must be bought and these can be pretty tight, these effectively allow the flight to operate a safe path through the air and all ATC regions. Most slots are in high demand and during the start of the season will often change. You will always notice Flight Deck and Cabin Crew pushing to get away on time this is to make the slot, a delay of even 10 minutes can cause this slot to be missed and the next available one may be 3 hours away.This also explains why day flights are much more expensive than deep night flights, the 'good' slots cost much more.
