This sounds like a problem born of players living in a society where corproations are too often considered good guys, or at least part of the establishment. Corporations rule instead of governments, but most players still end up towing the line. The boss is just different.
I have never played a prewritten Shadowrun adventure and one of my friends that really likes the game is decidedly anti-corporate in outlook. So we never served the corps so much as we would steal their tech and sell it to the highest bidder, or blow up some factory or whatever causing real harm.
The 'punk in cyberpunk is supposed to be supplied by the players.