When you reply to a message in Church Social using the web interface that comment is visible to all recipients of the original message. It is also automatically emailed to the message sender plus anyone else who has commented on a message thus far.
Our long term goal here is to help facilitate discussion between church members in the app, although I don't think that will be fully realized until we add push notifications to the app.
If members reply via email to the email message sent from Church Social, those are private between you and the original sender. We did this very much by design, as we didn't want personal information to be accidentally shared to everyone who received that message. When replying to an email, most users have the expectation that the message is directly between them and the sender to whom they are replying.