My brother and I did Passau to Bratislava in 2013 just after the floods.
Flew Easyjet to Munich, stayed overnight in a hotel in Freising close to the airport then train to Passau using a Bayern ticket [very cheap the more of you there are]. We picked the hire bikes in Passau, plenty hire options. The bikes are generally sturdy and well equipped bikes with hub gears and Ortlieb panniers, although heavy which you notice if you venture off the path up the valley sides [as we were wont to do]. We prebooked hotels on the route and found them all good value. We encountered several riders at the same hotels that were on the organised rides where their luggage was moved on each day.
You can't get lost on the path that is generally wide and well surfaced throughout. When in the towns or villages, the car drivers gave way to cyclists at all times. The route is flat and very samey most of the route up to Vienna, but lots of interesting places to visit along the way. The organised trips tend to end just outside Vienna taking the train in from Klosterneuburg. We cycled in to the centre of Vienna on the traffic free Donauisel and the cycle paths in the centre are easy to navigate.
We took the bikes on the train back from Bratislava to Passau - this involved three changes in Vienna, but no problem. For trips after that we have taken our own bikes, but it is probabaly cheaper to hire bikes in Austria than it is to take your own. We did buy the Bikeline book [in English] in Passau. It is excellent but generally used our smartphones for navigation.
Overall it was a very enjoyable trip.