When YT was skating away from a Fed Land building, someone launched a rocket at her and knocked her off her board. She went unconscious and woke up in a van with religious people headed to the raft. How did the religious people get her if she was still in Fed Land?
Short of hiding my whole answer I don't think I can answer without some spoilers. Anyhow, here we go:
The Feds are co-operating with Rife, and Rife is the power behind the Reverend Wayne, so although it isn't spelt out it seems likely that the Feds simply handed Y.T. over. In chapter 52 when Y.T. gets to the Core she says (well the narrative from her perspective says):
There's even a little helipad where the suits can come and go. There's a chopper parked next to it with a logo she's seen before: Rife Advanced Research Enterprises. RARE. The people who gave her the envelope to deliver to EBGOC headquarters. All of this is fitting together now: the Feds and L. Bob Rife and the Reverend Wayne's Pearly Gates and the Raft are all part of the same deal.
The feds were working with Rife. The evidence includes (not in chronological order): The EBGOC/RARE package to the US for which YT was specifically needed (they want to know her name, doesn't matter if it's unreturnable, "you're YT?" when she delivers, ch 41), due to interest in her ... because they know she is working with Hiro the hacker and probably also the mafia, and she escapes the 'falabala' park twice (the technology for that intel is easy), and she must know something about the Plan because she destroys her mother's Fed computer (mom's a Fed programmer), Ch. 37 reveals that YT's mom's job concerns a program about which she knows nothing except that there are a lot of people working on it. Then her mom is interrogated concerning her daughter's behavior. Later YT sees a RARE helicopter on the raft, and the President of the US gets in it with her once she's kidnapped. Doubtless there is more.
It is clear that YT is a small fish that is interfering in Rife's plan. She is young and relatively inexperienced, and thus easy to take in the course of her Kourier duties. Once captured by the Feds she is transferred to another of Rife's tools: Wayne's world.