Scout, speaking from the innocent perspective that she had back when the trial took place, remembers the "glare of hatred" in Mayella's eyes. Like the previous answer correctly noted, this glare was a very angry look that Mayella gives to Atticus, and to everyone else, really. It resulted from a variety of things. First, Atticus was able to demonstrate that Mayella was making things up to turn the blame on Tom Robinson. Second, he uncovered the chaotic dynamics of the Ewell household, including the questionable father/daughter relationship between Mayella and Bob. Third, Mayella was already angry and, in her low intellectual mentality, was sure that she was being made fun of, and that she was being disrespected by the people in court. While these things do not justify Mayella's behavior, it is interesting that Scout attempts to make logic of what she sees. 

Notice that Scout consistently makes observations about Mayella. Among these observations, Scout notices that Mayella must be a very lonely person, and that she has no friends or support systems whatsoever

When Atticus asked had she any friends, she seemed not to know what he meant, then she thought he was making fun of her. (ch 19)

She also notices that Mayella may have never been treated with respect by anyone in her life. Moreover, Scout is quite surprised that Mayella found it offensive that Atticus had referred to her as "Ma'am" or "Miss" in court. These ways to refer to women are quite polite and professional. Moreover, these are accepted ways in polite society to refer to a female. Still, Mayella is not part of this polite society, and she does not know what is acceptable behavior. In spite of all of this, Scout is able to put all the variables together. She develops empathy for the poor woman. These are signs of maturity from Scout's character. She is not just making conjectures based on what she can see at plain sight.