But we now know that atoms can be split and that they split into protons, neutrons and electrons. The protons and neutrons form the atom's nucleus.
Most atoms have the same number of protons and electrons and so have a neutral charge overall.
If an atom has more protons than electrons, it has more positive charge than negative charge, so the atom is positively charged. If an atom has more electrons than protons, it has more negative charge than positive charge, so the atom is negatively charged.