Eliza's deal expires soon so I doubt that was a factor. You could argue ROI, but I'd argue they got that with Dollhosue. The first 9 episodes all ranked high in the Nielsen C3 charts, which is indicative it performed fine for advertisers. Until the last few episodes, where it started to drop off a cliff.
Most of the series was profitable, I'm told, all said and done for FOX (network). They didn't spend $10m on the pilot (Firefly), which radically alters the landscape in terms of profitability. Add DVD, new media, international sales (20 countries now) and licensing for the studio and it will be extremely profitable for them. That's why 20th are taking more of the financial burden for 2nd season, away from the network.
I was stunned at the time it got renewed, if I'm honest. But I since found out the 13th episode got presented as a template for how to shoot cheaper - they shot it on a budget of about 1/3rd of the usual show cost. If they can hold the audience they have left, it'll stay profitable, so it'll stay around.
By the way, the deal that has been cut includes the option to order another back 9. Premiere is fall.