I keep losing this so I'll post it here..
Several newer distros don't allow you to run the simulator from the file manager anymore.
Gerrit 1987 adds a shortcut generator, for now it needs to be run manually
similar to ../tools/configure
run from your simulator folder
../tools/genshortcut.sh exepath shortname icon
../tools/genshortcut.sh ./rockboxui clip+sim music-app
Don't forget to give it execute permissions... chmod +x