Imagine you want to know the flux of bugs flying horizontally along a road.
If you count the number that go splat on your windscreen, then you'll collect less (in a given time) if the windscreen is tilted: the number will be greatest at 90º, and zero at 0º: it'll be proportional to cosθ.
Mathematically, flux of a field E through a surface with area A is E.(Añ), where ñ is the unit vector normal (perpendicular) to the surface.