The idea that all matter is made of very small indivisible particles is very old.
Robert Boyle’s study of compression and expansion of air brings out the idea that air is made of tiny particles with lot of empty space between the particles.
The smallest unit of an element which carries all the properties of the element is called an atom.
Experiments on discharge tube, measurement of e/m by Thomson etc. established the existence of negatively charged electrons in the atoms.
Because atoms are electrically neutral, a search for the positive charge inside the atom was started.