This has nothing to do with the vehicle type or whether you stop or
continue thru. Its about who owns the road. You are not paying for the
road use per se, you are paying to use the National Park.

Roads in most national parks are owned, maintained and controlled by
NSW National Parks & Wildlife Service, therefore using the road is
using the park and the entrance fee applies.

The Royal National Park is one of the few parks where the road going
thru the park is a gazetted road owned and maintianeed by local govts
i believe. Therefore if you just ride along the road no park fee is
required. If you stop and use the park, or possibly use certain other
roads that run off the main road, then you must pay the park fee.

The Royal National park is actually one of the most expensive National
Parks in NSW to drive a vehicle into:
http://www.nationalparks.nsw.gov.au/npws.nsf/Content/Daily+vehicle+entry+fees

In the past ive found a table which listed which parks you had to pay
to drive thru and which you didnt, but I cant find it now.

Sean