Well, but... yeah. I know people weren't targeting Linux in the early 2000's, that was the problem. That's what I'm saying.
One of the biggest advantages of dumping Flash was that it got replaced with a runtime that worked on every OS even if people weren't deliberately targeting it. I'm saying that's a big enough advantage that it's worth the tradeoff. The Linux market share on desktop computers was tiny back then, but it was big enough that the community deserved to have a web in its entirety that worked for them. Not just a couple websites, they deserved to have full access to the platform that claimed to be a democratizing environment, and they were never going to be a part of that platform as long as Flash existed.
I disagree that Linux compatibility back then was a non-issue. It was not. It was a serious problem that held Linux back as a platform and as a daily driver and we all hated it, and it feels very dismissive to say that it was just a tiny side effect or that it's irrelevant to the broader point. Flash was never cross-platform and it held back the entire web from being a universally accessible platform. And it only got fixed because developers were forced to use a runtime that supported Linux. That is the only reason that Linux browsers are usable today.
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I am kind of skeptical that distributing SWFs is actually that much easier than distributing zip files. Even downloading/stealing and re-hosting JS code is not that hard. This is coming from someone who agrees with many of your points about the overall accessibility that Flash brought. But I do not believe it's harder to distribute content on the web today than it was back then.
I uploaded SWF files to those portals, I put them on flash drives. My process today for distribution is pretty much the same. And once this stuff is on the web, the web is vastly better at distribution than the Flash Player plugin was.