There is another benefit aside from the one that miva2 mentions about the Clan Castle only being loot-able to 10% rather than the normal 20%.
This other benefit is that it can hold more resources than your current storage space allows. If you have max gold storage of 1,000,000 for example and currently have 900,000 and you win 200,000 then the clan castle allows you to store that extra 100,000 until you've spent the gold you have. Also you can only collect as much loot as you have room for in storage. So if in the previous example you collected from your clan castle 100,000 of those resources would go into your stores and the remaining 100,000 would stay in your clan castle