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.