It's very easy to confuse scientific frameworks with actual truth but these couldn't be more different. When a (good) scientist says that there is a "law" of gravity or that that "matter is made of elementary particles," he does not mean these statements literally.
In other words, nobody (with a clue) is going to tell you that the existence of elementary particles is a fundamental fact describing the nature of the cosmos. Instead, the various particles, laws, attributes and so on that physicists like to talk about are convenient notation. When they say
"Gravity affects all matter"
they really mean:
"If we describe matter in the contextually obvious conceptual framework, i.e., objects in motion continue their motion until acted upon by a force, etc., etc., and then imagine or pretend that there is a force which acts upon all matter in the framework according to the following equations, and call that 'gravity,' the results are highly consistent with our experience/perception which, presumably, is some kind of reflection of whatever it is that is really real in the cosmos."
Of course it would be ridiculous to always speak that way. This sort of shorthand (pretending it's all true) is good enough to fly airplanes and keep us high on adderall, so it's almost never necessary to think so carefully about these finer methodological points when we do scientific stuff.
See:
http://http://en.wikipedia.org/wiki/Hypotheses_non_fingo
The point is, nobody (except an idiot) is trying to say that you are literally made of atoms or molecules. That is not the message or consensus of science. All that science tells you is that it is very useful and expedient to
pretend that you are made up of atoms and molecules.