From the excerpt quoted by RedChili:
As of the inauguration date of the line and for a 90 day period thereafter, traveling from the Yitzchak Navon Train Station in Jerusalem will be free of chargeto any destination in Israel and back – only for those passengers purchasing a trip contract (train ticket) on a personal or semi anonymous Rav Kav card at the Yitzchak Navon Train Station in Jerusalem
... as I understand it, traveling will only be free for those who carry a Rav Kav (the multi-use public transportation card) and only if they pick up their free tickets in Jerusalem.
I don't know how it actually is going to work, but that's how I am reading those lines.