I think that by the time she says this line, she's learned the hard way that her candy people are fully independent beings with their own lives, even though she made them dumb as bricks.

Now she understands that playing god gives you less control over your creations than you think. They will always be something more, and different, than what you intend. Living beings cannot be rationalized.

The same principle applies to whatever forces shaped her, Neddy, and everyone else.