Ninite Updater is a $10 a year service aimed at home users, completely separate from their Ninite Pro offering. Ninite Free does not automatically update. The article was pushing Ninite as an alternative to Flash's built-in updater but omitting the fact that Ninite Updater is paid.
I would be interested to know how you propose using Adobe flash updater to push out a critical security patch to 10k + enterprise users.