It is true that if you exert a force onto the pebble by kicking, as long as the pebble is in contact with your foot, it will exert an equal and opposite force on your foot. But it requires less force to kick a pebble; as a result, the reactionary force is also small and therefore not painful. But you will try to kick a big rock with harder force as a large object requires a large force to break the inertia of rest. Therefore the big rock will exert equal and opposite force on foot, which now will be painful. It’s not that a big rock hurts more; you will use larger force for a big rock and in reaction, the rock exerts that large force onto the foot.