The deeper reason for why Hamilton's principle is true is mysterious within classical mechanics. It's just a mathematical observation that one can derive many equations of motion from a variational principle.
From the physical point of view you have to use quantum theory to understand why it holds true. If you formulate quantum theory in terms of Feynman's path integral in many cases it boils down to a path integral for the propagator of the particle over all paths with the action of the analogous classical system. In the case that the system is close to classical behavior, the action divided by [itex]\hbar[/itex] is very steeply rising around the classical path, along which it is stationary, and this means that the path integral is dominated by paths very close to the classical one, which explains why the equations of motion follow from the Hamilton's principle, which says nothing else than that the classical path is given by the stationary point of the action functional.