Then you've never lived in a rural area with animal herds. The Sheppard has a responsibility to take care of the animals, he doesn't ask the sheep if it's comfortable getting a shot.
Well in any event, the government did not in fact hold people down and vaccinate them like shepherds do with their sheep. They also don't shear us and make clothing from our hair, or butcher us for food. So the shepherd analogy isn't meant to be literal in every sense.