A little context is important to understand this quote.
Miss Maudie and Scout are talking about the children's obsession with Boo Radley. The topic of Mr. Radley comes up and Miss Maudie says that Mr. Radley was a "foot-washing Baptist." Her point is that Mr. Radley was too religious. Scout is confused at this point. Wasn't Miss Maudie a Baptist also? Miss Maudie says that she is a Baptist, but not a foot-washing baptist. In other words, her religious beliefs were moderate and not excessive.
Here is where your quotes comes in. Miss Maudie likens religious fanaticism to alcoholism. In fact, alcoholism is better than being too religious. And in the end, both are destructive.
Mr. Radley's problem is that he took the bible too literally and because of this, he ruined his family life. Later we learn that Boo was a casualty of this kind of excessive religious life.