[mseebach2]

"Super" means that the subject is "above" as in superstructure, superscript and superintendent. A supercharger is then a charger that's above (presumably in performance) regular chargers.

"To charge" means "to load [a carriage]", "A charge" means "a [carriage] load" -- so while the metaphor is overloaded, it actually seems to applies better to charging a battery than to forcing air into a combustion engine.

[sliverstorm]

If we go with your interpretation of "above", it actually makes perfect sense- the intake charge is "above" ambient pressure.