When building a pond with a rubber liner it it essential to line the bottom and sides of the excavated pit with something to protect the liner so that roots and rocks don't poke holes in the bottom. Several inches of sifted play sand, newspapers and old rugs work well. These will also act like a buffer between the weight of the water and anything that might work its way up from under the liner. 

Commercially produced underlayment materials are available for this purpose and the manufacturers will all tell you that newspaper and carpeting will rot away and eventually expose the liner to puncture.  While I do agree that the newspaper may eventually rot away, most modern carpeting will last indefinitely under a pond liner. (...and it is free!)  The only problem with used carpeting (other than it smelling like a pack of wild dogs peed on it the night before) is that it may contain small tacks, bobby pins, and other sharp objects which you need to carefully remove.

For this project wire mesh was added to protect from the larger stones and rubble that were exposed along the sides.   (as water was being filled in the pond liner I backfilled the gaps with a mix of Portland cement and sand)