The job of a tripod is to give a very stable base for your spotting scope. The two most important things to look for are stability and a very smooth head.
A carbon fiber tripod is generally more stable per pound than aluminum. The lesser weight allows you to have thicker, more stable leg sections than aluminum while keeping the weight in a range that you wont mind carrying around all day. Carbon fiber is not as effected by temperature as aluminum. Carbon fiber helps to dampen vibration before it reaches your spotting scope!
Cost. Generally speaking carbon fiber tripods will cost more than something comparable in aluminum.