We're a relatively poor city with an underfunded transportation system. If the city / state invested more money, there would be fewer system failures, cleaner transportation, on time transportation, safer transportation. But that's not to say it's entirely up to the municipality to improve the system. It's to say that there's a lack of enticement for a lot of people. If more people rode the system, we would see improvements.
There needs to be a huge revamp of the system with the key card being just the start of it. Perhaps the new signage will help too. The larger issue is PR. You're not going to get people from outside the city to ride in (ie: 76ers place) when all the news reports they see are about the bad things that happen on the subway.
SEPTA needs to be branded as the life blood of the city and marketed to everyone regardless of your financial situation. Philly's also a small city so you're more likely than in larger cities to rub elbows with people from a variety of personal situations, for better or worse.
What's frustrating to me is that I have family who live outside the city but close to a rail line (Trenton / East Trenton). They're hesitant to drive into the city because of a lack of parking. I have tried to get them to park at their local station and to ride the train in. I was doing it for a solid four years for family events when I didn't have a car. It's fantastic and I prefer it over driving.
I also have a friend who lives outside the city but near a regional rail station. He and his wife both work in the city just blocks from a subway station. They choose to sit in traffic over sharing public transportation. Part of it is convenience, some of it is the shared company, some of it is the unreliability. It blows my mind that someone would go out of their way and choose to drive the Schuylkill twice a day over having a leisurely pre and post work day experience.
The main thing that prevents me from riding SEPTA more often is the schedule. I work from home so 99% of the time I'm taking the train it's on the weekend. The weekend frequency is prohibitive enough that I bought a car.