My ENT thinks a lot of sinus infections are fungus based, too. She asks new patients to go on Ortho Molecular's Ortho Biotic Powder and Ortho Molecular's Sinatrol. With the probiotic, she thinks it's better for the sinuses to go with a powder you dissolve in water instead of a capsule.
When I first went to her, I did have fungus in my sinuses (ewww, right?). I went on the 2 recommended supplements.
Fungus never showed up again for me in my sinuses, so that is effective, but I'm still plagued by bacterial sinus infections. The problem I have is that almost anything natural I try for my sinuses has a horrid effect on my sleep. I do tolerate the 2 supplements she recommended, though.