A difference of opinion will surround this question. There are some that think Mayella may not be referring to anything more than the kisses most fathers give their daughters out of love, protection, etc. However, in the context of the questioning at the trial and the timing of Mayella's answers, there's a chance that Bob may have engaged in some inappropriate actions with Mayella. Did he rape her? Nothing real concrete is evident to support that, but there might very well be something more than simple physical abuse occurring at the Ewell house. If Bob had been involved in inappropriate behavior with his daughter, jealousy would have been another motive for him to legally attack Tom (and physically attack Mayella). Like most great stories, you'll get to decide for yourself what you truly believe, but there is certainly many questions surrounding this family that don't get answered very clearly.
There's no evidence to show that he did. Bob, looking through the window, saw Mayella grab Tom's legs and heard her ask him to kiss her. He called her a whore and threatened to kill her. Tom ran off, and Bob obviously beat her afterwards. Bob is such a racist bigot that he accused Tom of rape to hide what Mayella had done. Even as horrible as Bob Ewell is, he's white, and Tom has no chance against an all-white jury. This is the crux of the novel and explains how Tom is like a mockingbird. He felt sorry for Mayella and tried to help her. For that, he's found guilty, leading to his death. Chapters 18 and 19 contain both Mayella's and Tom's testimony at the trial. For more details, go to the link below.