Are you sure it isn't wind buffeting? It happens on pretty much every car that has some aerodynamic efficiency. Modern cars are much more aerodynamic than they used to be. Automakers try to guide the wind around the lines of the car. This means that wind is passing by your closed windows. When you open one, air rushes inside and creates the noise you are talking about. It sounds like a helicopter, but it kills your ears. Whenever I want the driver's window down while driving, I also open the front passenger window to balance the buffeting. It is more bearable that way. Or you could turn off the air refresher.
Why Do Slightly Opened Car Windows Make That Awful Sound?