This would work fine, but I'm not sure to what effect. To charge a 12v battery you need more than 12 volts (more like 15-16). Also, you'd only be able to charge one battery, but you would be pulling from four, so one of the batteries is going to die sooner.
It would also depend on how much amperage this generator makes at that speed. You'd need at least 2 A to get an effective charge going, and even then you're talking a slow trickle charge, extending range a bit more than charging it up for another trip.
It seems to me the best way to hook it up in parallel; that is, the system is only 48v, but when you're pedaling, the pull on the batteries is not as strong, some of the current is coming from you instead. This avoids unbalancing the pack, the higher voltage and amperage needed to charge a battery, and it increases efficiency too. Taking the pedal power and turning it directly into motion would be more effective still, but that engineering could be more difficult.