Stevie Wonder - Superstition Lyrics Meaning

Not very much "hidden meaning" here. It's all in the chorus, "When you believe in things that you don't understand, then you suffer"

It isn't just religion versus superstitions, it's anything. If you believe in your car but don't really understand how it works, it's going to break down at the worst possible moment. If you believe in the reliability of your job/the economy but don't really understand how business works, you're going to be downsized at some point when you least expect it. If you believe in the government but don't really understand how it works, you're going to become a slave. If you believe in money but don't understand it, you're not going to have any. If you believe in your relationship with your spouse but don't understand it or them, you're in for a nasty surprise one day.