The amygdala, simplistically speaking, is responsible for emotions such as anger or fear. So yes, Visions is absolutely right; the people are afraid because their amygdala is responding to information from their environment (Wanda blowing up buildings) and initiating fear.
Ok, but the amygdala doesn’t stop there. It’s also involved in the learning process. According to Ivan Pavlov’s idea of classical conditioning, learning occurs when an organism (an animal/human/android) begins to associate something with an emotion or behavior that were previously unassociated.
Say for instance, you feel hungry and then hear the clock chime twelve o’clock. This keeps happening, eventually you associate the two things, and then sometime when you hear the clock chime, you feel hungry in response.
This concept works especially well with strong emotions like fear. So say people see a building blow up on the news or in person. Naturally, their amygdala fire up, and they feel fear. But they also see Wanda and the rest of the Avengers at the same time they feel this emotion. Remember, the amygdala is sitting right on top of the hippocampus, where memories are encoded. The stronger the emotion, the stronger the association and the memory. The next time they see Wanda, even if no buildings are blowing up, people are very likely to have a fearful response.
The Registration Act – Individualist vs Collectivist values
Obviously, the main focus of Civil War is the division between the Avengers about whether to remain a private group, working outside and perhaps occasionally even against the law, or to begin working as a public organization at the judgment of the United Nations.
Tony Stark promotes working under the UN because he believes the supers should be held accountable to a higher authority. Steve Rogers, however, resists because he believes the supers would be signing over their personal responsibility and autonomy.