Working in a microbiology lab has given me a whole new insight into the sheer volume of bacteria out there. Chances are your kitchen counter is dirtier than your bathroom to be honest. For example, if tap water is filtered onto agar and left to incubate you would be astounded at how many different species of bacteria grow on there (don't mean to scare anyone!). I see no problem with using regular toilet rolls for piggies, they are exposed to much worse things just by living with humans that what you would find in a bathroom. Bacteria prefer moist, warm growing conditions, so as long as you don't leave them in the cage for too long, and provided they aren't wet then nothing dangerous should grow on them.