FlagMaker 2 is a complete rewrite of the original FlagMaker in Java for cross-platform compatibility.
Download a release from the releases page.
Run setup.exe, then run the installed FlagMaker.
You need a Java runtime as well as OpenJFX. The following will install the necessary packages on a Debian-based system:
apt-get install openjdk-8-jre openjfx
Then unpack the release .zip file to a convenient directory, change to it and run:
java -jar FlagMaker.jar
Instructions are forthcoming. You should be able to run the .jar file as on GNU/Linux. Feel free to document this here and submit a pull request with your documentation.