The survey was a joint project between Monash and the ACU; I think it's fair to be concerned about bias. However, I wouldn't at all be surprised if people involved in organised community religion participate more in the community, if only through having many more opportunities to do so.

Intuitively it makes sense that more young people would be atheists than before, but if we don't have those comparable figures, how can we be sure?

You're mistaken about the survey questionnaire, which is available online for your perusal.

ETA: So is a summary of the findings.