Why the overall charge on an atom is zero

This is because the number of protons and the number of electrons in an atom is the same.

An atom usually includes protons, neutrons, and electrons. Each proton carries a positive charge, no charge for neutron, and each electron carries a negative charge.

The number of protons and electrons in an atom must be the same or else the element will no longer be an atom but an ion instead, which in ions, they carry different charges depending on how many electrons they have lost/gained. The number of proton is never changed because it is like the identity of an element.

Therefore, since the number of protons and electrons are the same in any atoms, so the overall charge is zero.