You're right that there is nearly always a negative overtone to this expression.
Let's say you have a horrible boss at work. One day, you and your colleagues are chatting to a new colleague on her first day, and she says that she thinks that the boss is really nice and friendly. Afterwards, when she has left the room, someone says 'Do you think we should tell her the truth?', and you might say 'Oh, don't worry. She'll find out soon enough!'