FlyDamage.java

package com.colt.flydamage;

import org.bukkit.Bukkit;
import org.bukkit.entity.Player;
import org.bukkit.event.EventHandler;
import org.bukkit.event.Listener;
import org.bukkit.event.entity.EntityDamageEvent;
import org.bukkit.event.player.PlayerQuitEvent;
import org.bukkit.event.player.PlayerToggleFlightEvent;
import org.bukkit.plugin.Plugin;
import org.bukkit.plugin.java.JavaPlugin;
import org.bukkit.scheduler.BukkitRunnable;

import java.util.ArrayList;

public class FlyDamage extends JavaPlugin implements Listener {

    ArrayList<String> protectedPlayers = new ArrayList<String>();
    Plugin plugin;

    @Override
    public void onEnable() {
        Bukkit.getPluginManager().registerEvents(this, this);
        plugin = this;
    }

    @EventHandler
    public void fallDamage(EntityDamageEvent event) {
        if(event.getEntity() instanceof Player) {
            Player player = (Player) event.getEntity();
            if(event.getCause() == EntityDamageEvent.DamageCause.FALL) {
                if(protectedPlayers.contains(player.getName())) {
                    event.setCancelled(true);
                }
            }
        }
    }

    @EventHandler
    public void toggleFlight(PlayerToggleFlightEvent event) {
        final Player player = event.getPlayer();
        if(event.isFlying() == true) { // don't ask why this works
            protectedPlayers.add(player.getName());
            new BukkitRunnable() {
                @Override
                public void run() {
                    protectedPlayers.remove(player.getName());
                }
            }.runTaskLater(this.plugin, 200);
        }
    }

    @EventHandler
    public void playerQuit(PlayerQuitEvent event) {
        Player player = event.getPlayer();
        if(protectedPlayers.contains(player.getName())) {
            protectedPlayers.remove(player.getName());
        }
    }
}