While being unable to clear your ears can be uncomfortable, real pain comes from fluid trapped in the sinus cavities. This can come close to feeling like having a dull, rusty 1/4" drill bit run slowly into your face.
Flight surgeons have recommended a good blast of Afrin or three and sudafed in the past.

If you are having trouble clearing your ears it is best to stay out of aircraft with high cabin climb/descent rates or freefall jumping.