Anybody who carries their boards on a soft roof rack will know all about the howling noise it can make, especially when its windy. Before I got my new board, I used to carry my old NSP Board and sometimes up to 2 others on a Ocean Earth Soft Roof Rack.
Firstly ensure your straps are tightened well and that your board(s) are securely fastened. The trick is to bend the piece of strap between the soft pad and the door into a c-shape with your fingers. While bending the strap, wrap the insulation tape around it a few times to keep it in shape. Try and have the c-shape facing the back of the car.