I'd never heard of MonoDevelop, and it seems to me this article was really scrounging to create a sense of its "primacy" that isn't real.
Neither sfbay-craigslist, Indeed, or SimplyHired come back with any job listings that mention 'MonoDevelop'. Meanwhile, even combining the three terms [linux eclipse java] gets multiple hits at Craigslist and over a thousand each at Indeed/SimplyHired.
There's a fair chance that Eclipse itself is the most popular Java desktop app on Linux. (Developers aren't blocked by outdated Debian packages nearly as much as the article implies, and the article's claims about what was missing in Eclipse 3.1 are false.)
Azureus and LimeWire have also been widely-used Java desktop apps, on Linux and elsewhere.
There are lots of people using Linux to develop Java, but that doesn't mean they're using Java to develop desktop apps for Linux. Mostly they, like you, are using it to develop server-side web apps, I think.
I think the article is correct that most people aren't choosing Java for new projects they start. I assert without evidence that the Java job listings you see are primarily for existing projects. I wouldn't be surprised if you chose Java for a new project, but it seems like most people prefer Python or Ruby or C# or, for some things, C.
There's not much standalone desktop Java anywhere; it's clunky for that purpose. But the article is claiming some sort of Mono/MonoDevelop ascendancy for Linux desktop apps, and that's not in evidence.
For example, I'd estimate the usership of Eclipse and LimeWire on Linux as larger than any two of the Mono apps mentioned in the article or this thread.
'linux eclipse java' would net you all the server-side Java roles. This article is about desktop app development.
If the most popular Java desktop app on Linux is an app used exclusively by software developers, then Java indeed has issues creating end-user apps, as there are far more Linux end-users than there are developers.
Interestingly, on both Mac OS X and Ubuntu, Eclipse is the only app I have to wait for a context menu to pop up when I right click a project. It is also the only Java app, as Android (what I'm developing for) has different UI libraries.
Neither sfbay-craigslist, Indeed, or SimplyHired come back with any job listings that mention 'MonoDevelop'. Meanwhile, even combining the three terms [linux eclipse java] gets multiple hits at Craigslist and over a thousand each at Indeed/SimplyHired.
There's a fair chance that Eclipse itself is the most popular Java desktop app on Linux. (Developers aren't blocked by outdated Debian packages nearly as much as the article implies, and the article's claims about what was missing in Eclipse 3.1 are false.)
Azureus and LimeWire have also been widely-used Java desktop apps, on Linux and elsewhere.