Well, the current FOX regime has already shown itself to be supportive of genre shows with questionable ratings. They gave Dollhouse two seasons and aired all its episodes (except "Epitaph One," but that was a special case) despite shaky ratings that would've led a previous regime (say, the ones in charge at the time of Firefly) to cancel it halfway through season 1. Maybe they've learned from their predecessors' mistake with Firefly and have come to appreciate the value of a loyal fanbase for a genre show, so they're trying to cultivate those fanbases rather than alienating them. Maybe they just really respect the work of creators like Whedon and Abrams and want to give them every chance. Maybe they like having critically acclaimed shows on their network as a matter of prestige. (We saw a similar dynamic at NBC under Brandon Tartikoff in the '80s. Quantum Leap would never have survived without his personal enthusiasm and commitment toward it. Sometimes network executives do have priorities beyond ratings alone.)
And part of it is clearly that they recognize that Fridays are not going to be a strong night ratings-wise, so they have to lower their expectations. Fringe has done better for them in that particular time slot on that particular night than previous shows did, so that makes it a plus for them.
Fringe has an interesting arc, and even in the episodes of lesser quality, there's generally at least a few great Walter moments to look forwards to. Bring on season four!
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