Usually, when people say that humans (and organisms in general) are 'machines', they mean that they function through a series of physical reactions. In this way, everything is a machine, as well as composed of machines, as well as part of a machine.

You draw a comparison to computers and point out their simplicity, and that is true. The human brain is millions of times more complex than current computers, from the circuitry down to the molecular level. Yet the point is that they function on the same principles of causality, however more complex one may be than the other.