Hi Laura:
When I first moved here, I took the train on a regular basis to go to my Spanish classes in Hato Rey (Piñero Station). I would take the bus from Condado to the first station (Sagrado Corazon) and then over to Piñero. There was a big parking area at Sagrado Corazon. I never felt uncomfortable or unsafe. Our class went to the fruit/vegetable market in Rio Piedras (two stations down from Piñero) and that was a lot of fun. On the way back from class, I would sometimes get off at the Hato Rey station and take the ferry back into Old San Juan (I think it was $1.00 per person). It was a neat way to see the old city from the water, especially if there are big ships in the harbor. However, the ferry is out of service at times, and there is no way of knowing until you get up to the ticket counter.
If you go, you can get a metro card that can be used for the bus as well. The last time I used one, they honored transfers. I've gotten info from the Puerto Rico Day Trips website, so that may be a resource for you too.
Hope this helps. Enjoy your trip!