No, you do not need to add a ferrite bead between your VCC regulator output and the VCC pins on the FPGA. There are two reasons for not adding the ferrite bead, the first being that the VCC pins are less susceptible to power supply noise so they do not need the ferrite bead. The second reason for not adding the ferrite bead to the VCC connection is that with the rapidly changing higher currents required by VCC, the ferrite bead may allow the VCC voltage to briefly sag and go below the minimum recommended VCC voltage specified in the datasheet for normal operation of the device.