They're not as delicate as they look. It's just fine to gently shampoo and comb your tot's hair and scrape off cradle cap scales.
They're also not stationary. You may see a soft spot pulse right before your eyes, rising and falling as blood and bodily fluids pass through it. This is totally normal.
They are clues to illness. A soft spot that remains sunken for more than a few minutes, especially when accompanied by vomiting, diarrhea, and/or fever, can be a sign of serious dehydration, so get to the doctor or emergency room ASAP.