We know that all matter are made up of atoms and all atoms consists of electrons ,protons, neutrons ,etc.Then why do we find such a variety of matter?Why is wood not gold?

Answer 1

Why such a variety? Because of the large number of ways (currently about 115 or so elements) that electrons, protons, and neutrons come together to make elements AND the almost endless variety of ways elements come together to form compounds.
Second question. Gold is gold because the number of protons make it the only element of its kind; wood is not an element but a compound composed of elements. The bottom line is that Au is an element and wood is a compound.