I use Alignment only as a way to identify supernatural connections. If you are Chaotic, you have tied yourself to the Chaotic forces in some way or shape, and therefore are also affected by spells that target supernatural/Chaotic powers. Same with Good/Evil (which I define as Creation/Destruction).
For example, a Lawful Good character has tied themselves to two Major Powers, one of Order, and one of Creation. The extreme of this is something that uses rules and patterns to stop death, destruction, creativity, change, and anything related. So Protection From Good will work against the PC, as will anything that targets Lawful creatures. Chaotic Good favor change and creation, the extreme being a constantly changing storm of new ideas and thoughts without permanent form. Good and Evil balance by creating and destroying, Law and Chaos balance by natural laws and change. Neutral are the raw elements that everything is made of (Earth, Air, Fire, Water), which are both constant and changing, creating and destroying.
Most people are neutral (small n), with no clearly defined supernatural ties. They may be altruistic, self-interested, psychotic, or have a secret fetish on a Friday Night, but none of that affects the ability of spells to affect them so therefore I leave all of that to roleplaying.