This was/is one of Java's mistakes. It's always been oddly hostile to JVM bundling, although some projects do so anyway (e.g. Jira). More generally, Java makes the mistake of making itself known to the user. The user is expected to install a JVM, rather than one being bundled with the application, and they're then expected to ensure it updates itself appropriately, complete with an annoying taskbar icon and always-resident auto-updater (on Windows, that is).
The user shouldn't even know the word 'Java'. Applications written in Pascal, for instance, are just applications. The user isn't made aware of the technology used.
Especially unfortunate considering that, as far as I can tell, JavaFX is really a pretty good GUI toolkit (I've only dabbled). Perhaps things will change as ahead-of-time compilation for Java becomes more mainstream.