The Move Silently rules apply unmodified regardless of your mode of movement. This is because they only reference "your normal speed", which can be any speed (land speed, fly speed, etc.). This means you make the same amount of sound when flying as when you are moving across solid (not noisy) ground.
Refer to the Invisibility Special Ability for rules on how invisible creatures are pinpointed. The following clause is especially relevant for purposes of locating invisible creatures by hearing:
A creature can use hearing to find an invisible creature. A character can make a Listen check for this purpose as a free action each round. A Listen check result at least equal to the invisible creature’s Move Silently check result reveals its presence. (A creature with no ranks in Move Silently makes a Move Silently check as a Dexterity check to which an armor check penalty applies.) A successful check lets a character hear an invisible creature “over there somewhere.” It’s practically impossible to pinpoint the location of an invisible creature. A Listen check that beats the DC by 20 pinpoints the invisible creature’s location.