Got information from someone from BAE System. They retract flaps after landing to minimize the ingestion of debris and other foriegn object inside the wings. There is is alot of delicate hydraulics, screw jacks etc with need to be protected. Note that they do it as soon as the aircraft is off the runway.
Airline flap settings for take off are max15-20 degrees. Landing is generally 30-40 degrees. Keeping flaps down would probably result in more accidents!!