It's because Yomi ship's effect doesn't target your monster. It just destroys whatever battled with it. It only works if your opponent has to manually choose a target for one of their effects, like michizure or metalmorph.
Card is garbage and a noob trap in this game. The chances of you having Lord of D, a good dragon, is damn near impossible. Either I draw lord of D early on with no flute or the flute, D and no good dragon.
try using Yami Yugi skill Destiny Draw, or Sorcery Conduit (make sure to keep Lord of D. as the only spellcaster in the deck). pretty easy to succeed if you balance your deck right. it's even possible to get TWO good dragons, Lord of D., and a flute in the second/third turn.
"Blue Eye Whaito Dragon!!!!" Tell you something? The single role of Lord of D is to summon blue eye and protect him of traps. But is obvious a third rate duelist like you isnt able to see the real power of the cards.
omg I converted both cards I don't have them anymore. I just started this game and I didn't know wtf I was doing obviously. Now that I know the game a bit better I see what a noob I was :(