creamegg:
What your daughter is reacting to is a pressure change. Whilst aircraft are "pressurised", it's not the same pressure as ground. So it's like being taken up (and down, finally) to about 5000 ft or so, depending on what the crew dial up in the cockpit.
Most people (and children) will be fine, bar a few usual side effects like 'blocked' hearing. In rare cases it can be painful. If your daughter suffers from this frequently, when flying, then it might be worth a trip to the GP, just for peace of mind.