Assim:
@Override
public boolean onCommand(CommandSender sender, Command command, String label, String[] args) {
if (sender instanceof Player) {//Ve se o sender e player
Player p = (Player)sender;
if (label.equalsIgnoreCase("fly")) {
if (p.hasPermission("vua")) {
if (p.isFlying()) {
p.setFlying(false);
p.sendMessage("§cFly desativado!");
} else {
p.setFlying(true);
p.sendMessage("§cFly ativado!");
}
} else {
p.sendMessage("§cSem permissão!");
return true;
}
}
}
return false;
}