people have two very different mechanisms for making decisions. one is fast and heuristic, the other slow and logical. they are described in great detail in the book "thinking fast and slow" - http://en.wikipedia.org/wiki/Thinking,_Fast_and_Slow
the reason for the discrepancy between emotion and logic reported by the person you're talking to (and more or less anyone who's not incredibly autistic) is because emotional responses tend to be connected to the first (fast, unreliable) mechanism which picks up on things like apparent injustice (but ignores, for example, calculations based on supply and demand).
so it's quite normal to feel something that is at odds with what you would logically expect.