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. 

Miss Maudie's remark to the children in Chapter 5 of Harper Lee's To Kill a Mockingbird refers to the fundamentalists-the "foot-washers," who drive past her place castigating her for her abundant flowers.  According to Miss Maudie, the foot-washers thought that she spent too much time outdoors and not enough inside the house reading the Bible.

When Scout remarks that Miss Maudie is the "best lady" she knows, and wonders why Mr. Arthur does not come outside, too, if he were "hankerin' after heaven," Miss Maudie interjects that Scout is too young to understand.  But, some people take things to extremes, thus making something intended as good into evil.  By taking the Bible literally people misuse scripture and sometimes make it fit their own twisted intentions.  This perversion of the words of the Bible is worse than whisky in Atticus's possession--it does more harm.  For, they take the word of God and make it serve their purposes; for example, the "foot-washers" think that women are a sin by definition, Miss Maudie says.  Taking the Bible literally, these people see all women as Eves and other people as threats, possibly.  Arthur Radley is kept inside the house because Nathan Radley, Arthur's guardian and brother, does not allow him to go outdoors.

To understand what Miss Maudie means, let's look at the context of their conversation.

Scout and Jem are talking with her, a lady whom Scout describes as a trusted, intelligent adult:

"Jem and I had considerable faith in Miss Maudie. She had never told on us, had never played cat-and-mouse with us, she was not at all interested in our private lives. She was our friend."

The kids are trying to understand why Boo always stays inside his house, and Miss Maudie is trying to explain. She starts by mentioning that Boo's father was "a foot-washing Baptist," meaning someone who's so religious that they take everything from the Bible as literally true, and they think anything fun at all is a sin--like planting flowers instead of sitting inside to read the Bible. They even think women are sinful just because they're women.

That's when Miss Maudie delivers the line about the Bible being something destructive when one person uses it--more destructive than alcohol when someone else drinks it.

What she means is that some people use the Bible not as a way to gain wisdom and understanding, but as a weapon to restrict people's lives and demand that they act a certain way. Miss Maudie seems to be hinting that Boo's father was that zealous about his religion, and as a result he was so demanding about the things Boo could and couldn't do, that Boo felt immobilized (frozen) and suffered some kind of mental damage that resulted in him staying inside his house all the time.

Miss Maudie was trying to be clear when she said that the Bible was worse when one man wields it compared to if Atticus were to drink alcohol--she was trying to explain that religion, improperly interpreted and forced on someone, can be worse than if someone just gets drunk and treats people terribly or violently. But the kids don't really understand the comparison; they get stuck on thinking about how their father doesn't actually drink.

In general, Miss Maudie means that there are some men (and women) who claim to be good, caring, Christian people. They claim to be good people because they are religious. However, simply being strictly religious does not necessarily make a person good to other people. Miss Maudie is speaking particularly of Mr. Radley (Arther's/Boo's father). Apparently, Mr. Radley is a strict Baptist, but he is actually quite rude with other people and downright abusive to his son. On the other than, take someone like Atticus Finch. He is not as strictly religious as Mr. Radley, but Atticus is much more considerate and generous towards other people. Even if someone like Atticus were drunk, he would still be much more kind than someone like Mr. Radley. Miss Maudie clarifies this for Scout in the next paragraph: 

What I meant was, if Atticus Finch drank until he was drunk he wouldn’t be as hard as some men are at their best. There are just some kind of men who—who’re so busy worrying about the next world they’ve never learned to live in this one, and you can look down the street and see the results. 

Atticus is a good person regardless of how devout he is. Likewise, Mr. Radley is a troubled, even "bad," person in spite of being quite religious. Using Miss Maudie's example, a blind drunk Atticus is a better person than a Bible-quoting Mr. Radley. In general, a drunk, kind person is better than a religious abusive person. The additional problem here is that someone like Mr. Radley might even justify his rude/abusive behavior by claiming religious superiority. 

What is the significance of the statement about the Bible and whiskey in To Kill a Mockingbird?

"But sometimes the Bible in the hand of one man is worse than a whiskey bottle in the hand of—oh, of your father."

In Chapter 5, Miss Maudie is having a conversation with Scout regarding Boo Radley's past and family background. Miss Maudie explains to Scout that Mr. Radley was a very strict individual, and was a "foot-washing Baptist" (Lee 59). Maudie tells Scout that "foot-washing Baptists" believe that women are a sin by nature and that anything that people take pleasure in is considered a sin. Maudie also tells Scout that Mr. Radley took the Bible literally. She attempts to use the following analogy to explain to Scout that people can use the Bible to support their negative beliefs by saying, "but sometimes the Bible in the hand of one man is worse than a whiskey bottle in the hand of---oh, of your father" (Lee 60). Scout is too young and naive to understand Maudie's analogy. Maudie is trying to convey that fact that some people misinterpret the Bible and use the scriptures to support their intolerant and ignorant beliefs. In Mr. Radley's case, he interpreted the Bible literally to keep Boo Radley inside of the house and away from the public. His decision to shelter his son negatively affected Boo Radley's life, similar to the way alcohol can negatively affect a person's well-being.