If my belly/abdomen/part of my body generally around my belly button/tummy/etc. hurts, I say "I have a stomach ache." It doesn't necessarily mean that my actual stomach (the organ) hurts, it's more a general referral that my belly/abdomin hurts.
When I was a kid and had a "tummy ache" I thought it actually was my stomach, not now I know there's a lot more down there than just a stomach, but when it hurts, it's more socially acceptable to say "I have a stomach ache" than to say "wow, my large intestine is really hurting!" ;)