Your best bet is going to be EQing it to sit in the mix. See what boosts at about 500, 1k, and 5k sound like and if any of them individually or a combo helps it sit in the mix more.
That said a lot will depend on the band setup and the composition of the song. If you have guitars, bass, keyboards, vocals all going for it and leaving no space, both literally and sonically, there’s not really much you’ll be able to do to stand out. If the flute part is really important then more considered songwriting from the other musicians will be important to give it a platform to come through.
You could also run it through an EQ with a graphic display and see where the fundamental tone is coming through and ask the other musicians to make an EQ cut there.
