Not only can a musical instrument work, but anything can work. Seeing as magic only works if you believe in it, then suffice to say wands, staffs, or anything else can be used. Everything has energy, what makes certain items work better then others for certain people is the fact that the energy of the item is in sync with the person. If you want to use the flute do it, but cleanse it first then insert your energy into it.
Placing it in moonlight for a night works for cleansing it and so does placing it in the freezer over night. Once it's cleansed, meditate with it and picture your energy flowing into it and see the intent you have for it flow with your energy into the item. Hope this helps