Emotions are really complex reactions to events. The way I understand it, very simply, the brain perceives an event and then assigns it a positive or negative rating, filters it away into a memory bank, and draws on that memory as needed. Most of our memories are but a few seconds long. For example, our brains don't need to maintain the memory of walking down the hall. More important events, like who spoke to us in the hallway and what the conversation was, is stored in more long-term memory and emotions are assigned according to all kinds of past experiences. That explains why we think of Grandma fondly but feel apprehension when thinking about the dentist.
It is my understanding that we react to an event, feel an emotion, and rationalize our feelings and reaction in the split second it takes for us to process this combination of perceptions (thus the concept of "free will"). So when we say we're acting logically rather than emotionally, it simply means we can justify our response logically. But then, I think that when we react illogically, that too can be explained logically because the brain makes these choices based on a logical process. Jumping in front of a car to save a toddler is logical because the brain registers the possible negative effect of doing nothing and watching a child die against the positive effect of knowing a child will be safe. This reaction is biological, which isn't logical or illogical but well, biological, but we can explain it logically because of that. This wouldn't work for people with mental health challenges, of course.
One of the problems superstitions have is they seek to explain logical reasoning through illogical means. Being trained to accept and protect superstitious thinking would mess this up, and I think explain people like Fred Phelps or Michelle Bachmann.