I'm not quite sure what you mean in this case, because the atmosphere hasn't really been in perfect balance ever. However there is a general answer that I'll try to set out.
Essentially the point is that balance is not magical but quite the opposite: it's desirable. In most if not all physical situations you can imagine starting things off in whatever starting condition you like, then sitting back and watching how things progress. Almost invariably the system will try to reach a balance. It's just easier, in some sense. Things are usually more stable, or it takes less effort to maintain the balance. This idea (or a variant of it) is one of the guiding principles of physics, and amounts to saying that "nature wants to take it easy".
At any rate it is no accident that, if left alone long enough, everything reaches a state of balance. The same is true for the atmosphere, for example. ("Left alone" doesn't mean "left alone by humans", but by anything that isn't part of the normal state of affairs. Asteroids colliding, or volcanic activity, also disturb the system.) What happens next, when you try to disturb the balance, depends a lot on how the system is set up. It's possible for a balance to be ideal and the system could easily return to it no matter how hard you try to move away; but in many cases the balance is just not stable and even a small kick will change things significantly. Unfortunately, the atmosphere is in the second category and is sensitive to change.
Not sure if that clears things up but hopefully it helps a bit. The point is that balance is nice, so that you'd expect to see it eventually, but not always easy to maintain.