Why do humans flinch when they think they’re going to be hit or something is coming at them?

Explanation:

All animals (including humans) instinctively flinch when they feel threatened. In tests on monkeys, researchers identified a region of the brain that they call the "polysensory zone" that appears to be involved in flinching. This region responds to various different stimuli (visual, sound, and touch) and may be involved in the physical behavior seen during a threat.

Flinching happens in two phases. First, there is an initial startled reaction to stimuli -- the air puff. Next comes a longer defensive response designed to ward off the threat.