The "El" is the MFL, the Market Frankford Line, one of Philly's two subways. It has a reputation for crime and unsanitary conditions, though how bad it actually is very debatable. Going to Penn you can bypass it entirely from most areas of the city.

RR is priced based on distance, but the cost doesn't actually vary that much - I believe the possible range from PA destinations is $4-7 per trip so not as extreme as other cities. There are also monthly commuter passes available.