In Chapter 18, Mayella takes the witness stand. Mr. Gilmer begins his questioning and Mayella bursts into tears. The judge allows her time to compose herself and asks her who she is afraid of. She points to Atticus. She is afraid Atticus will make her look like a fool. Or worse, she is afraid that Atticus will expose the truth. The truth is that she seduced Tom, Bob Ewell caught her in the act, and then Tom ran off. The logical assumption (probable truth) is that Bob beat Mayella himself and made Mayella accuse Tom of the beating.
So, while Mayella is afraid of Atticus for reasons stated above, she is really afraid of her father. She does not come right out and say this, but it is the truth. She is testifying against Tom because her father put her up to it. She is afraid that Atticus will expose the truth. The real threat in her life is her father. It is generally acknowledged in Maycomb that Bob is a drunk, abusive father. Atticus almost gets Mayella to admit this. Atticus asks if Bob is easy to get along with. Mayella says he is tolerable "'cept when--" and she does not finish her sentence. Atticus replies with what everyone knows, "Except when he's drinking?" Mayella nods in the affirmative, essentially saying 'yes.' Atticus presses her and asks if Bob has ever beaten her. She denies it, but she says this because she is afraid of Bob. Had she been questioned in private, without her father present, who knows what she would have revealed.