In most circumstances, the last factor (the cosine of the angle) is equal to one because the direction of the force is usually the same direction of the displacement. But in circumstances like pushing a heavy box at an angle not parallel to the ground (let's say pushing it at 20° towards the ground), the direction of the force is not the same as the direction of the displacement. In this example, because of the angle of the applied force, the force is doing less work because it is not as efficient as pushing the box at an angle parallel to the ground.