The scientific method does need to posit natural cause in order to form a working hypothesis but research method does not equal reality. As an example, the chemist must posit a chemical reaction in order to form a working hypothesis in chemistry. This does not mean that reality is limited to chemical reactions, he is just limited by his research method. The same is true of the natural sciences as a whole.
There are many reasons to reject the existence of the supernatural, but these are metaphysical propositions, not science.
Just as the expectation that the sun will rise tomorrow is a metaphysical supposition.