It is a good question which can be explained by a very easy and common example.

Suppose you have a ball and you put it the ground. Now it's in most stable condition. Now you raise the ball to some height, let's say X. It's now somewhat unstable and now you have raised it further more, let's say it 2X. It's very unstable now.

You would have seen that as POTENTIAL ENERGY INCREASES STABILITY DECREASES.

And the case is same with atoms. They combine so that they can increase their stability and when they increase stability, Potential Energy decreases. It's Natural

I hope you understood:)