As we live our lives we are constantly taking new information in from the environment around us. This is all taken in from the different senses that we have (sight, sound, smell, touch and taste). Some may argue that we have a sixth sense of sorts. Think about as you are walking along minding your own business and you have the feeling someone is watching you. This is an odd thing that happens, not sure if it has been studied, although it would be interesting to look at. Anyway on with how we take things in through our 5 perhaps 6 senses. All of this information is then sent to our brain where the brain begins to muddle through what it thinks is important and what it doesn't have time to deal with at the moment and other things that it just ignores. Those things that we decide to think about and actually look into are then filtered through our own past experiences, emotional state at the moment, and active thoughts. Out of all of this mess comes our perception of the situation.
Now if we add another person to the situation who is going through the same process we have two individuals trying to make sense of all of the things going on. This can cause some confusion. Now if we add to the mess two people trying to understand each other and make sense of everything and on top of that they are both hiding something or are on guard for what ever reason. Perhaps one of them wants to impress the other or there is a power differential between the two. Now we have a very big mess. If we add on top of this any type of mental illness or extreme defensiveness it just keeps getting worse.
Now that we have the mess above going on it is easier to understand how perceptions can be warped when a person first meets another person. This understanding of the nuances and problems that can occur between our characters can give us tools in how we want our readers to perceive our characters as well. Keep in mind that as our readers are reading our stories they are having all of these things going on with them as well as they meet our characters and get to know them. They will expect them to act a certain way and they will react differently based on their own past experiences. For this reason it is important to make sure that as we are writing we keep in mind how we want the reader to react to our characters and build them based on the expected outcome. We will not be able to predict every perception of every reader but the better we understand people and how they behave the better we can understand how the majority will react. For example most readers are going to be sad when the little boy in our story gets beat. However, some readers may have an experience in their childhood where they were beaten by their father when they got an 'F' on a report card and feel that it made them better. They may then have little sympathy for the child or at the most may feel that the child should buck up and get on with it. (This is extreme of course).
The better that we can understand how people will perceive our characters the easier it is going to be for us to manipulate emotions from our readers and get them to feel the way that we want them to feel. This will also help us when we are trying to get sympathy for our characters making the experience of reading our book that much greater.