Despite it being one of the most popular and feature rich download managers out there and it being foss, it seems that most repos don't have it ( except for flahub iirc) Is there is any reason behind that?
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It's only popular among people who download frequently from filesharing websites. Most Linux users don't, hence why it's not available on any of the default distro repos.
In fact, I'd say the act of downloading regularly from filesharing websites, has largely gone out of fashion among the general public (obviously I'm ignoring the underground/illegal/niche scenes here).
For the most common types of large files which Linux users might manually download - eg ISOs, movies, TV shows - torrents are generally preferred, and torrents have very capable native clients already, such as qBittorrent.
For other general large files manually downloaded via http (eg Linux ISOs, tarballs of packages etc), these are already hosted on legitimate websites (like github) which don't impose any artificial download restrictions, so your browser, or any "normal" download manager can handle them just fine. For these sort of downloads, aria2 is the most popular third-party downloader in Linux. aria2 is a command-line program, but there are many GUI frontends for it too, such as uGet and AriaNg. There are also browser addons that integrate with aria2. Aria2 is also native and very lightweight, so again, there's no need for JDownloader here.
TL;DR: Most distros don't offer JDownloader because most Linux users don't actually need it.