the AI (who is behind me in naval tech) is always trying to kill my cruisers (strongest naval unit) first.
And although a cruiser can survive several attacks, it isn't immortal.
so, what to do?
well, (I should mention at this time that I've got Magellans) in stead of sending a 2 cruiser patrol, i sent a cruiser/submarine patrol to any the AI.
My cruiser checks things out towards the enemy shoreand then pulls back, the sub lies waiting underneath the cruiser or one square behind it.

The AI comes storming out of his shipyards and attacks my cruiser (at least half of his attack fleet is short on MP and fails to attack)
next turn, my sub mops up the strongest enemy ships and the cruiser takes care of the rest.
if eigther ship is badly damaged, replace it and leave the other one in place.