DH and I were in Cairns this past September.
We went there in order to join a liveaboard scuba diving cruise, which was absolutely fantastic. Everything was incredibly well organized and the crew was extremely knowledgable and friendly. I could definitely recommend the company we went with, but there are quite a few out there which I am sure are excellent as well.
We found Cairns to be a beach town without the beach. The city itself is very dull, mostly tourist information and restaurants, and if you want to do anything of interest you either have to go out on the reef or inland to see the rain forest or rafting. All of these activities we found to be very expensive.
We did a guided rafting tour, half-day which was great, but opted out of additional guided tours - we prefer to look around by ourselves. What we did do was take a hike to Mt. Whitefield which was very nice, but due to the heat and humidity was relatively hard, and then we took a look at the botanic gardens which were also very nice.
I'm sorry we didn't take a cruise out to Green Island or Fitzroy Island, but my husband was dying to get out of there.
The highlight of his trip was the Northern Territory, which was our next destination.
In September the days were hot, and the nights cool. Out on the reef the nights were downright cold and during the day there was a wind blowing which was chilly for me (but then I'm from Israel so anything below 25C is cold...)
In short, I would spend as much time as possible out on the reef. The experience I felt I missed out on in Australia is the whole beach experience. We got to Sydney in mid-October and it was grey and drizzly, so even Bondi was depressing.