A number of factors.
Programming
If it ain't broke don't fix it (cab drivers especially)
Service costs
The initial rumour of the box being programmed to self destruct at 300,000kms thus requiring a total rebuild (this scared a f**k of fleet operators away from the ZF).

At the end of the day the 4 speed box is a bucket of s**t compared to what else is on offer today. They tried to address the s**t with the 5 speed but it was a failure because it had the same sloppy shift quality as the agricultural 4 speed. Still better than the commodore but still a bucket of s**t. Ford have finally achieved the goal of having world class engines in their cars and to fit them with anything less than world class transmissions is a travesty.

sure the zf 6 speed auto is better than 4 speed, but repair costs are much higher if needed to be replaced. i have heard that 6 k is what zf are worth. im much happier with my 4 speed that is much more common and cheaper to repair, or replace., in my bf 2 xr6.