This is a potent question. I think it can start to be answered here, but more and thorough examination from different points of view will be needed. In my mind, the femme fatale depiction of women is influenced in great part to how men can see women. The standard "evil woman" depiction feeds the femme fatale conception. This is one in which somehow, women possess some elusive ability to control men and manipulate them. This might be through sex, tantalizing wares, or rendering them weak. For example, in Gilda, the Rita Hayworth character is able to inspire an intense level of irrationality in both her husband and the Glenn Ford lover character. Both men are shown to be desirous of her in a manner that inspires a lack of clarity in action and in judgment. Such a depiction of women makes it easier to pigeon- hole or stereotype them as almost like sorceresses. This is something that cinema has been able to advance because it finds an audience.
On some level, the femme fatale characterization is evident in films because the audience validates this through purchasing tickets or affirmation of a particular film. Where I think that the femme fatale characterization is also advanced is that the development of plot and enhancement of a film's conflict can be helped through a femme fatale character. For example, in Body Heat, the Kathleen Turner character's femme fatale qualities are what drives the plot for Ned to understand her true nature, albeit too late. The writer and director of the film end up insisting on the femme fatale characterization to help move the plot and advance conflict and climax. In a plot shrouded with twists and turns, the femme fatale characterization can help to move this along, making it more of a need in films. In doing so, though, a definite stereotype about women and how they act is evident. Again, this is validated by the audience and the media and through this validation, the insistence is seen repeatedly as a way to generate profit. These might be reasons why the femme fatale characterization is insistent in many films.