You could do a working GUI with the JVM. But most people demanded Windows desktop apps, and for Windows only you could use .Net and C# for a better experience. Linux community was in big part against Java or Mono because of license and FUD so Python was the winner for the higher level language there.
Firstly let me state that yes, you could make a GUI with Java but it would suck because the GUI toolkits available at the time were just downright awful (and they still are!). Want an app that's super bloated and looks awful (no native controls)? Use Java!
Also, the Linux community wasn't against Java per se (not until Oracle bought Sun anyway) it's just that writing Java was a huge/complicated undertaking compared to say, Python and managing JREs was a huge pain in the ass. The old joke was, "By the time you have Eclipse open I will have completed the program in Python."
Lastly, mono was enormous (and still is)! Talk about bloated! When mono was being most actively pushed on the Linux community back in the day there was just no benefit: For smaller things you had shell scripts and Python. For larger programs you had C/C++, Java, and... Python :D. Why would you go through the hassle (and it was a huge hassle) of using mono when those other languages provided better performance with much lower friction/barrier to entry? It didn't have much of a "selling point" as it were.
From my memory there were anti-mono communities, and anti mono packages that would force a conflict with mono to help people not install mono by mistake.
It was not "use Python over C# because Python is better" the message was "Do not use C# because the language is open but the .Net frameworks is not open" and this is true, Mono implemented non open stuff and Microsoft did not offered a guarantee that they support Mono and won't cause troubles from companies using it. Fuck MS, they had a good language and a decent platform in .Net and Silverlight but they had to prioritize what Windows team wants to we are now stuck with JS and Electron.
Sure Java apps start slower then C apps but I am talking about Pro apps, an app you start in the morning when you start your job and close it when you are done, I don't care is a bit slower. I am also playing games in Wine and when I have foudn modding tools in Java that work natively in Linux I thank in my mind the dev that he was not a Java hater.
But yes, Linux communities most of the time did not care to have theyr apps to work or look native in Windows. So today if I would like to make a quick and dirty Linux app with a simple GUI I am not sure what to use, maybe Electron it would probably give me less issues as a dev(but this is personal opinion since I dislike Python syntax and I don't like to go low level if I don't have too)
