What matters is the art and not the gender. If you are good at what you have chosen you will be appreciated irrespective of whether you are a man or a woman. There is a general misconception that the flute is a very difficult instrument to master. It is no doubt not as easy, as say, the Violin or the Veena, but women can definitely master it. One needs to be highly innovative and creative.
Talent is very essential.
The flute has nine holes and the variations in the octaves can be brought about only by voice modulation. Conditioning the mind to bring out the required tone is crucial. To maintain continuity while playing the gamakas is very difficult. This comes only with practice. The other reason why the flute is probably not very popular is that the instrument requires very careful maintenance.