Cyclone V LVTTL GPIO Termination
I found 47 Ohm series resistors connected to GPIOs, they are using
  3.3V VCCIO


There are two reasons that I know of for putting series resistors in line with GPIO pins: -


Generally the cyclone family (that I've used) are very unforgiving of signals that may exceed 3.7 volts and the current limiting resistor is almost always a good idea. I've seen forums where Altera folk do recommend them on the basis that overshoot and ringing can exceed the 3V7 and cause the device to latch-up and possibly fail.
The second reason is when driving data - it acts as a termination resistor at the sending end of the data and prevents sustained corrupting reflections when the receiving end is open circuit.