I like to use a spaced pair of KM84s, about 8" apart, 4 feet away, 2 feet above the flute and angled down towards it.
If the flautist is particularly breathy, you can mic from behind to use the head for some acoustic shadowing.
It's important to remember that the sound is not coming from the mouthpiece. The sound radiates omnidirectionally, so if you were looking at the end of the flute, the sound radiates concentrically.
Hope that helps.