You imply Ninite are charging for Flash, but they are not. The charge is for the Pro service. I don't use it (I use the free installers, and love them). I'm not in the target group for the Pro--admins that need to keep a lot of machines up to date. If I were in that group, I'd gladly pay.
The whole focus on Ninite charging is a red herring. This also has to do with the free installer that Ninite provides to people who do NOT pay for the Pro.
The article was talking up the fact that Ninite allowed you to update your apps. The Ninite Updater, intended for home users, is a paid service for $10 and is separate from Ninite Pro, intended for corporate users. Without paying the $10 fee, Ninite doesn't provide automatic updates.
The whole focus on Ninite charging is a red herring. This also has to do with the free installer that Ninite provides to people who do NOT pay for the Pro.