Indeed, modern airline design has minimised the risk of the problems you speak of which result from a change in atmospheric pressure that occurs as an aircraft changes altitude. This condition is called barotraumas and is caused by gases trapped within the body expanding or contracting as the cabin pressure changes. The most common problems occur with air trapped in the middle ear or paranasal sinuses by a blocked Eustachian tube or sinuses. Pain may also be experienced in the gastrointestinal tract or even the teeth (barodontalgia).
There are two reasons passengers in modern airliners are less prone to these conditions. One is that there is much better control over the cabin pressure and the other is that modern aircraft design and materials allow higher pressurisation of the fuselage.
Obviously, atmospheric pressure decreases with height. In an ideal world, from a design perspective, the cabin would be at atmospheric pressure throughout the flight as this puts less strain on the airframe. From a passenger comfort point of view, the cabin would be maintained at ground level pressure throughout the flight but this means the cabin would be highly pressurised (relative to the outside) so would be under considerable stress.
As a compromise, commercial aircraft cabins were pressurised to maintain an internal pressure no less than that found at 8,000 ft. As the aircraft prepares to land and descends from its cruise altitude below 8,000 ft, the internal cabin pressure begins to rise. The cabin pressure continues to increase until landing to equalize the internal pressure with that of the external atmosphere.
Modern aircraft have much better control of this adjustment of the pressure during the descent so the effect on the human body is less traumatic. Also, more importantly, the designed operating cabin altitude for modern aircraft is much lower and this almost eliminates these physiological problems. For example, the Boeing 787 maintains a standard cabin pressure equivalent to an altitude of 6,000ft and the Airbus can maintain a cabin altitude as low as 5,000ft.
One disadvantage of the higher cabin pressure is additional costs. Amazing as it sounds, the extra weight of air in the cabin adds considerably to the running costs. Concorde had a specific problem with this as it flew at high altitude (60,000 ft.) while the cabin altitude was maintained at 6000 ft. This made the vehicle significantly heavier and contributed to the high cost of a flight.
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