Basically, the executive gets paid more because, at the very least of it, the executive is the paid fall guy. Secretaries only rarely have careers go radioactive because of things that are out of their control; executives have that problem quite often.
Executives get paid more, if for no other reason than because they assume more responsibilities and more risk.
There is also an expectation that the executive is more valuable than the secretary; while this isn't always true, if you didn't expect the executive to be more valuable than the secretary, why the hell didn't you hire the secretary instead?

Oh, and there's also the fact that the executive pay scale is set by... other executives.