One is in for a long day when drifting a stream during low water
conditions in a pontoon boat. The tough abrasion resistant material
that covers the air bladders also sticks fast to the rocks on the
stream bottom, sometimes to the point that you have to get out of the
boat to move it.
I share your concerns with protecting the pontoons from damage. In
fact, I have implemented a few strategies to reduce the friction
between the pontoons and the rocks with little success. Ultimately, I
have come to the conclusion that the best strategy for moving through
skinny water is to simply get out of the boat and walk it through the
shallow riffle.
If the water is at a level that calls for a great deal of walking over
the course of the trip, perhaps, it is best to leave the boat at home
and walk in. It is best for the longevity of the boat and the stream
bottom.

Richard