Because flash was a plugin, not locked to that one little game. Once you install it, every website could use it. A lot was done, by browsers, over the years to try and give more control to the end-user, but Adobe didn't have too much interest. They were the dominate player, what other option was there!? Countless security vulnerabilities (https://www.cvedetails.com/vulnerability-list/vendor_id-53/p...), siphoning personal data back to Adobe, etc. Looking today at what some companies are doing to harvest data, one could say they were just ahead of their time...
I'm sorry, I don't understand why. If someone develops a fun little game in Flash, and then I play it on Kongregate, what harm has been done?