WD,
Rottnest, AKA Rotto (and that is what you better call it if you want people to know where your talking about), is a great little spot.
You can walk from the airport to the 'village' in maybe 10 mins, or a free shuttle bus comes past every 20 or 30 mins and takes you to the village.
I dont know the who's who of JT anymore, but if there are only 2 of you, then most of the operators will have something suited to your needs. I use to hire off JFC and Air Australia.
When you finally get to the Island, you will no doubt want to do a 'boggy' lap of Rotto. Try to avoid flying low over Thompsons Bay (eastern part of the Island) as this is where everybody is. You can get bikes for hire from here also. It is getting bl00dy hot here and it will take you a few good hours to cycle around so take bucket loads of water as there is nothing (or not much) once you leave the Village area.
One last thing, Quokka soccer is only fun for the dead beat drunken yobbo schoolies
