Rooftop solar systems are generally of little harm to the roof, especially if non-penetrating racking system is used. The question of protecting your roof is only relevant to the subject of flat rooftops.
Recently there’s a general tendency in the industry, both by the system installers and system owners to use protective mats under solar systems. If you are considering penetrating racking then using protection can be a little difficult. On the other hand, protective mats lay nicely and easily under non-penetrating rackings on flat rooftops.
There are few materials that are used as sacrificial layers for the roof. The most common are EPDM sheets that are widely available. These are reliable solutions and are very easy to be laid on the roof, and fall in the middle of price range for protective mats.
Other options include polystyrene foam sheets and modified bitumen. The former might no withstand outdoor environment in the course of twenty years, although being cheaper compared to other materials. Modbit might a little more expensive, and not as available as EPDM.