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.