The issue is having AppGameKit libraries appropriate to the platform you are running on.
This applies to the Android platform as well. Java is only a small piece of that setup. Most of it is still C++ libraries.
If/when someone decides to do a Linux version, they would need to build a library set and core file set specific to Linux setups. I would think it wouldn't be too hard, but it would still take time. And the AppGameKit developers are working pretty hard just trying to clear up bugs and get the next release with new features out. And, hopefully getting the other platforms discussed on the site up to date.
So, probably no AppGameKit of Linux any time soon.
Cheers,
Ancient Lady
AGK Community Tester