The two main concerns with carbon use are
1) what carbon takes out of the water
2) what carbon releases into the water
Everyone's familiar with how activated carbon adsorbs stuff. The concern is that this adsorptive capability applies to beneficial substances as well. 'Trace elements' aside

, a certain amount of organic glop isn't necessarily a bad thing --as many reef critters can eat the stuff.
Poorly made activated carbon can leach phosphates, sulfur and tars into your reeftank. The former can encourage unwanted
algae blooms. The lattest can irritate corals.
Good-quality activated carbon DOES have its place in a reef tank. I just prefer to use it as an emergency treatment.
Inthesand's post above provides one example. When corals and other livestock show signs of distress --the sort that leads me to suspect toxicity in the water, then sure I'd reach for the old AC just to lock down some of the offending substances in the water. But I can't keep throwing carbon at the problem (too expensive for me, hehe), sooner or later I'd have to hunt down the problem's source and neutralize it.
hth,
horge