This discomfort is caused by a difference in pressure between the middle ear and the outer ear across the eardrum.
One way to get over it is to try swallowing (or chewing gum, as has been suggested) as this tends to help open up the eustachian tube connecting the back of the mouth with the middle ear, helping to equalise pressure.
A better way is to do the Valsalva's maneuver as this forces air to open up the eustachian tube more reliably than moving your jaw in swallowing.