I like to interpret $f(x)$ as meaning $f\circ x$, otherwise known as the pullback $x^*f$. For instance $x$ could be the standard real valued coordinate on a line. This makes rigorous sense of the concept of a "variable" and hence also dependent and independent variables ($y=f(x)$). In the example of functions on a line, $f'=dy/dx$ is simply a ratio of 1-forms.
Such an interpretation also answers the common complaint that $f=f(x)$ confuses a function with its values. Instead it represents the very common shorthand of omitting pullbacks!