The whole circuit from the linked page is poor. For example I see no reason for the MOSFET part of the circuit. For charging supercaps a switching voltage regulator is much better. But if you can waste the huge amount of energy and are able to withstand the heat safely linear regulator may be used:
Set output voltage of the LM317 to a value safe for the supercap. Add a current limiting resistor between 12V and input of the LM317. If you want a "charging complete" indicator simply use a comparator to turn on the LED when voltage over the resistor is sufficiently small.