And my usual quasi-rant about SEPTA's treatment of visitors who're not familiar with the system: if you plan to ride more than once, make sure you look at various fare options that will give you a break on the full-cash "sucker fare" that many tourists unwittingly pay. If you're taking only the train ( = Regional Rail) be sure to either buy tickets in advance* or if you can't, be sure to get the surcharge refunded at any Center City ticket office. For buses, trolleys, and the subway (= Transit Division) you need to buy tokens** ahead of time to avoid a 45¢ extra charge. If you want to see more of the system, investigate an Independence Pass that will let you ride both parts of the system for a day, subject to some limits.
As far as things to see, you'll definitely want to see 30th Street Station*** where SEPTA and Amtrak meet, and try one of the Chestnut Hill lines to see the 19th-century heritage of the PRR or RDG. If you can make room for a traction-day, look at Route 15 which is equipped with renovated PCC cars. Also ride one of the subway-surface trolley lines from Center City out through West Philly. Take the Market-Frankford El to Upper Darby and visit 69th Street Terminal, where two of the original four suburban Red Arrow trolley lines still operate. The 101 to Media is fascinating as it goes through semi-wooded areas and ends up on State Street in Media, the only suburban town in the country that still has a trolley on its main street. Also try my favorite line, the Norristown High-Speed Line (still known to most of us as the P&W [Philadelphia and Western]), one of a tiny handful of interurban light-rail lines still operating.
(*) Or in SEPTA's dubious grammar, "advanced" (??)
(**) Another of SEPTA's homages to the 19th century
(***) 30th Street for now, but probably will be renamed by some corporate sponsor
Requiem for it's/its, your/you're, than/then, less/fewer. They were once such nice words with such different meanings...