This article is a bit... lacking. First off, the Flash updater on Windows works quite well on modern Windows systems. Second off, Ninite isn't just some good Samaritan, they're a for-profit company. Third, and related to the second, Ninite's updater costs $10 a year while Adobe Flash's built-in updater is free. They also have a Ninite Pro version that supports remote updates and installs and costs $240 to $2,220 per…
On an ideological level, I would look at whether they are stealing content and reselling it or just automating something the user would do for him/herself. It sounds like automating to me.
I make scripts to automate my workflows all the time, including the flash installer. (Though I don't download it as part of the script, I have pre-downloaded it and put it in a folder to use. So I have to manually get the latest before I run the script on a batch of machines.)