I'd think it means that if you run into someone who is different from you, you shouldn't be wondering "what's wrong with him" and instead should appreciate that all people are different.
I don't really like that message, though, because while it seems like a nice thing to believe/say, there are times when we run into someone who has behavior that isn't just different from ours - it's just wrong. For example, if I happen to be someone who is polite to others, and I run into someone who is always rude to others; I'm going to be asking, "What on Earth is that person's problem?!!" That's not a matter of my not understanding why someone, say, would like blue when I like green. That would be a matter of my running into someone who had out-and-out rotten behavior that I wouldn't understand. It would be natural for me to start wondering if the person had some problem that was making him so miserable and grouchy. In fact, I may even decide to overlook his bad behavior because I understood he could have some reason. I wouldn't happen to think this individual was a "mystery to revered". Instead, I'd see him as a rude grouch to be avoided or confronted (one or the other).
So, as with a lot of sayings, I think this one has its points but doesn't apply all the time (but maybe that's just me).