Adding to the list of places where manual transmissions are still common - I still see them in a lot of Japanese kei trucks[1]. These are super minimalist trucks used for agricultural and other jobs that cost less than $7,500. Upgrading to a CVT transmission adds an extra $500 or so to the price - which seems worth it to me - but when you consider that a lot of the work these are used for is low-margin to begin with, I can understand why people want to keep costs down.
I think manual transmissions are increasing in popularity though as a lot of farmers are aging, and lose confidence in their ability to operate a manual transmission.