Put a wind deflector on, see If that will help with the wind noise. Had to make up some custom brackets as the Thule supplied brackets wouldn't fit OEM roof rack. :
OEM Base Rail System (Roof Rack) and Thule Cargo Box + Thule Fairing - BMW 3-Series (E90 E92) Forum
Amazon.com: Thule AirScreen Fairing, 32", Black : Automotive
Amazon.com: Thule AirScreen XT Wind Fairing, Black : Automotive
Thule Airscreen - 38-inch - Wheel & Sprocket | One of America's Best Bike Shops
Thule Fairing (44" Large) Wind deflector reduces noise and improves mileage at Crutchfield