The D&D aligment is very expressly absolute. In D&D, Good and Evil are real universal forces that do not change depending on who is looking at them. An Evil creature might rationalize himself as being good, but he is just deluded. He is still Evil. Good and Evil exist and have a D&D definition. It is not up to debate.
It doesn't really mean that for other cultures/monsters, Good is good. Far Realm creatures can call A Foo and B Bar and have Protection from Foo spell - after seeing that Foo is causing bodily harm to them.
But the argument is from a perspective of language.
Your spell is called protection from evil, but does that mean it's actually protection from evil?
They're very, very few, but they are there. There's a paladin PP power that does more damage against evil things, there's a helmet that can only be used by LG/G characters, and in one of the Scales of War adventuresSuch as?
The alignment is a map. You are located somewhere on it. Your opponent is located somewhere on it.
If two people from the same segment battle each other, they can call themselves good and the opponents evil until their voice is hoarse; the aligment spells still won't work against each other.
Renaming the segments of the map does not move the map. The same actions and beliefs still mark you as belonging to a specific segment, no matter how much you argue against it, no matter what you'd like to call the segment you are standing on.
But Pelor is evil.
And Paladins are evil.
See, my protection from evil spell works against them!