Experimental results that changing the type of electrode or the type of gas did not affect the ray produced, led to the conclusion that electrons were part of all forms of matter.
The deflection toward positively charged plates demonstrated the negatively charged nature of electrons; the fact that changing the type of electrode or the type of gas used in the cathode ray tube did not affect the ray produced led to the conclusion that electrons are present in all matter.
We know that an atom is composed of electrons, protons and neutrons. These fundamental particles are arranged in a regular manner to form a stable atom.
The negatively charged particles, electrons are placed in fixed energy levels which are known as orbitals around the nucleus. The nucleus is placed at the centre of the atom and comprised of protons and neutrons.
Overall an atom is a neutral entity due to a similar number of electrons and protons in it. But this picture of the atom was not known earlier. Different scientist gave their contribution in the development of atomic models.
The discovery of cathode rays proved the presence of negatively charged particles which are known as electrons. Similarly, the existence of anode rays proved another fundamental particle of an atom that is known as a proton.
That time concept of radioactivity was well known and studied by various scientists. The existence of the nucleus was proved by Rutherford with the help of a Rutherford atomic model. He worked on Gold foil by bombardment of alpha particles and proved the existence of a mass body at the centre of the atom.
Read discussion about the earlier models like Thomson’s model and Rutherford's on atomic structure at chemistry.tutorvista.com.