The MetroRail Southern Suburbs line is an affordable, scenic, and interesting way to travel from Cape Town down to Simon's Town. Is it the most comfortable way to travel down the peninsula? Maybe not, but if you're used to using any large city's public transport, you'll do just fine. You can purchase a ticket at Cape Town Station on Adderly Street (one-way or return trip). Make sure to check the timetables because trains run less frequently on weekends. Do not take the train after sunset.
There are two classes - First (MetroPlus) and Third - with little visible difference between the two (other than fare). Third Class can be a little uncomfortable and often feels like you're stuck near one another like you're in a can of sardines. First Class is advisable to tourists and new riders. When leaving Cape Town station, the very first train cars closest to the station are First Class.
While riding the train, keep all of your valuables hidden and use discretion when taking photographs. If you notice MetroRail staff walking through the train during your ride, they may ask to see your ticket. When exiting the train, some stations will ask to see your ticket (and punch or initial it) and some stations will be empty. There is a fine if you are caught without a ticket, however.