Ever since the game came out the C2 has been noted for the damage it takes to put it down. Here are a couple of threads from way back when discussing the same thing:
http://subsim.com/radioroom/showthread.php?t=120743
http://subsim.com/radioroom//showthread.php?p=173955
It's my understanding that the major supermods, especially GWX and NYGM, go a long way toward fixing this, but using the Merchant Fleet Mod helps the most simply by giving so many more ships to target and reducing the chance of meeting any one type.
If you're playing SH3 unmodded you need to fix that first.