A refugium is a tank filled with macroalgae and microfauna (tiny animals) that is away from your main system. The primary purpose of a fuge is to give you a more natural means of getting the bad stuff out of your tank water and also to give a place for all that microfauna to grow. The microfauna means free food for your fish, the macroalgae means that they filter out things in your water that you don't want, like phosphates.
Also, if you put the fuge on a light cycle that is opposite of the light cycle on your main tank, it will help to stabilize the ph and the co2 levels (among other things) in your system so there are no night time/daytime swings.
I hope I didn't get too technical and that this helps you understand a little more about what a refugium is. IMO, there is no reason not to have a refugium as part of your reef system. They do all kinds of good things for you, and they do it in a natural way.
Stacy