Frankenstein approached his project with the vision that creating life would be beautiful and the result would be incredibly exciting and wonderful. As the creature comes to life, he sees the horrific creature for what it is, an amalgamation of body parts and organs from dead humans and he is disgusted. He flees the house to get away from his creation, this terrifying creature.
It is not difficult to imagine that a common reaction to a creature like this coming to life would be similar to Frankenstein's. The image of a patched together, half rotten being suddenly coming to life is a frightening one that would terrify almost anyone.
And it is not just the physical shock of such a creature but also the idea that life has been created in that sort of a creature as opposed to the normal baby or small animal that we expect to be the representations of new life.