Movement of molecules and working of fan are two entirely different concepts.
Fan causes a wind chill effect by circulating more air faster around your sweating body so that evaporation at higher rate takes off body heat. You feel cool.Fan is not cooling the air in the room.
Instead it is forcing an air current towards you.
Fan drives the air current towards us , not disturbing the kinectic energy of the molecule , as size of fan is very large as compared to that of molecules (infinite approximation). So we feel cold during wind.
Temperature rise due to kinetic energy increase of molecules running around at approx. 500m/s are not very profound.
Hence when an air current is forced at us, we feel cool as the air current absorbs heat from our body, not because fan creates cool air or something.
Hope you get the point.