FT232RL VCCIO Question
The datasheet does say in "Absolute Maximum Ratings", 


  DC Input Voltage – USBDP and USBDM: -0.5 to +3.8V
  DC Input Voltage –
  High Impedance Bidirectional: -0.5 to + (VCC +0.5)
  DC Input Voltage
  – All Other Inputs: -0.5 to + (VCC +0.5)


RXD/TXD should be okay driven by a 5V device, they are operating below their absolute maximum. 

It is common for signals to be below 5V.   

What is connected to RXD/TXD? 


  Voh, Output Voltage High, is only min: 2.2V, typical: 2.7V, max: 3.2V


at VCCIO=3.3V, which might have a bearing on your decision. 

Edit:
Some 5V devices might like about 2.5V, so someone might get unlucky, and have a FT232R device with a minimum of 2.2V, and get unreliable results. This will likely be rare, but maybe intermittent, and hence unpleasant to debug.

I think Daniel's answer covers the input-pin case.