Zoidberg: I still don't know what cloackin is good for: it still isn't up long enough to make a huge difference to me. 
  Precisely, the trick is to keep it short.  
 The flagship's real dangerous weapons are : his missile launcher (easy to disable with a teleported crew, although less immediate when you've got to break through a zoltan shield first), his phase 2 special weapon (drone swarm), his phase 3 special weapon (some sort of projectile blast). The special weapon strikes are announced by "power surge" detection. That is when you must cloak. It has to be short, in order to just protect you from these power attacks, and to recharge between them. If you sync your short cloaks right, you have nothing to fear from them. And with enough shields and evasion, you have nothing to fear from the regular weapons - except the missiles if you didn't destroy its launcher yet. So, getting a good protection from the flagship is not that difficult.  
 Getting weapon combinations that harm the flagship is more tricky, but fortunately, there's a huge diversity of possible approaches there. And with decent protection (and staying attentive to power surges), you've got all the time in the world.   
 And if you asked about the usefulness of the cloak system in general : long cloaking allows you to recharge your weapons while your opponent's weapons don't. It offers you the first shot, and, on the long run, slows down his firing rate relatively to yours. But in my opinion, against the flagship, it's better to reduce the cloaking device's power down to 1.