Yep, I took one of those Quicksilver catamaran thingies out of Cairns. It ran up to Port Douglas before heading out to the reef. By the way, I saw (and swam with) a whale shark while I was out there. It was just a baby–about 14 feet long.
Saw some neat giant clams, too.
PS- That travel agent discount was definitely a good thing. My flights, my diving, and the Quicksilver trip were free.