More specifically, perhaps, Miss Maudie "ravels the thread" from the woven fabric of the Radley family. That is, she begins by pulling the small thread of what is known about the Radley family--Mr. Radley is a "foot-washing Baptist," a very strict, rigid fundamentalist who believed that any pleasure was a sin. And, according to Miss Maudie as she "ravels the thread," he interprets the Bible to suit his mean intentions. As she continues her ponderings on the household of the Radleys, Miss Maudie takes what she already knows and unwinds the thread of this knowledge and conjectures that some things that may go on "behind closed doors" might be unspeakable:
'The things that happen to people we never really know. What happens in houses behind closed doors, what secrets--'
'Atticus don't ever do anything to Jem and me in the house that he don't do in the yard.'...
'Gracious child, I was raveling a thread, wasn't even thinking about your father....'
While little Scout has missed Miss Maudie's point, she does recognize that, unlike Mr. Radley, there is nothing clandestine or hypocritical about her own father.
Literally, raveling a thread would mean to pull a thread out of a piece of cloth that the thread has been woven into -- what we would usually call "unraveling" it. But that's not really what Miss Maudie meant when she said that.
What she meant was figurative. She just meant that she was taking a thread of thought and pulling on it. She was taking an idea and just going over it in her brain.
Specifically, she was thinking about how things go on behind closed doors that people would be horrified to know about. When Scout says that Atticus never does anything bad to them behind closed doors, Miss Maudie says she was just "raveling a thread" -- sort of thinking out loud.