Physics studies many other things than just atoms, electrons, and molecules. (For example, it also studies light, gravitational and electromagnetic waves, black holes, expansion of the Universe, heat, other elementary particles such as W/Z gauge bosons or Higgs bosons, and lots of other things.) Or to say the least, it studies other aspects of matter than just their composition from atoms or molecules (when it studies heat, it's about the energy carried by atoms but it is interested in completely different properties than just the arrangement of atoms inside molecules). One should realize that all the known forms of solid, liquid, or gassy matter is composed of electrons, protons, and neutrons – or from atoms and/or molecules (different levels of description).
Chemistry studies very specific things: the phenomena in which atoms in molecules reorganize into different molecules (reactions) and the structure of these molecules as an organized collection of atoms. It studies it because it wants to convert materials, liquids, or solutions to others, usually because these materials or compounds have some applications. It is a modern scientific version of alchemy that began with this research in not-quite-scientific framework. While chemistry is very advanced today, it doesn't use mathematics too much.