Though, I guess you could say it was fate too based on what you've said. I think the past events, when explained, will say more about that. I also heard there's a prequel manga out or something too.The show makes it pretty clear she's piloting the Vox Aura because it shot her in the ass when she was drowning 10 years ago and she remembers that she's more or less bound to it, and it to her now. Though she wasn't privy to the conversation, when they were talking about it in the control room, they specifically said that once "Memoria" is established between Vox and pilot, only that person can pilot it from that point forward.
I get some Xenoglossia vibes from the relationship that Madoka has with her giant robot. I'm guessing this robot won't be Madoka's boyfriend though.
I guess i'll wait for more backstory (if that happens) to really see what's up though.