Upon thinking about it, I think the origin of the gear as an icon for the settings options must be the metaphorical "workings" of the program - the hidden mechanics, the "nuts and bolts" or the "clockwork" of it; as my spouse commented, it's hard to make a simple, iconic representation of a microchip, and USBs have the circuitry symbology nailed down already. But the clockwork metaphor is a simple and easily accessible one, even though we have very little actual clockwork in our everyday lives any more. Fascinating to think about.