There are alot more issues at play here.

One is security.

One is image(ala the bill gates story mentioned before)

Another is scheduling, including last minute
changes.

Another is ego

Most of the big Fortune 500 own several corporate jets. IBM has both Corporate jets and helicopters.

At the CEO level, the time=money equation adds up fast. All that check-in time would be very costly indeed.

Long flights would typically be working flights, with the ability to communicate both voice and data globally. On a commercial jet they wouldn't have access to scrambled communication available. It would be a serious risk to discuss business, not with the possiblity of electronic snooping on their airfone calls and all us nosey flyertalker sitting their in FC.

In 85 or 86 microsoft probably wasn't a fortune 500 company yet.