Lots of flights take polar routes -- I remember a brilliant view of the pole from a EWR-HKG flight once, on a sparkling clear day (when other pax, were scowling coz i had my shade open to see... In mid afternoon).

A friend who used to fly those routes told me they never fly right over it, but always a few miles offset. Concern is that at the pole all lines of longitude converge, so it could confuse the nav systems -- even though they're programmed and tested for it, don't want to take a risk.