TL; DR They don't have to - ions do exist, but relatively rare compared to the number of neutral atoms and molecules encountered in everyday life, and relatively short-living.
There are different ways to look at this problem:
Electron cloud
If we consider a single atom, then its electron has a probability distribution around a nucleus (one can always choose our system of reference to be centered at the nucleus). Since the electron cloud stretches infinitely far away from the nucleus, the atom appears approximately as neutral only when we look at a Gaussian surface of a very large radius (as compared to the atomic radius, i.e., the average thickness of the probability cloud).
Discreteness of charge
Another possible starting point is the charge quantization: since charge comes in units of charge equal to that of proton and electron, the non-neutral atom must have an excess of at least one proton or one electron. For an atom with an excess electron one can then calculate its stability as compared to that with no excess electrons. Of course, negatively and positively charged ions exist and often stable, but they easily lose or acquire the excess/missing electrons when interacting with other atoms. The parameters of the interaction are such that the neutral configuration is simply more stable.
Macroscopic charge neutrality
An object containing many atoms will attract excess charge till it becomes neutral, which is why collections of many ionized atoms are rarely observed. Also, a collection of ionized atoms would not be stable due to repulsive Coulomb interactions, which means that neutrality of charge is a condition of stability of macroscopic objects.