FTDI ft232rl 3.3V logic interfacing PIC microcontroller
Answer straight from the Datasheet:


  VCCIO
  +1.8V to +5.25V supply to the UART Interface and CBUS group  pins (1...3, 5, 6, 
  9...14, 22, 23). In USB bus powered designs connect this pin to 3V3OUT pin to  drive out at +3.3V levels, or connect to VCC to drive out at
  5V CMOS level. 


So Yes, if you connect VCCIO to the 3V3OUT, RxD, TxD etc. will all be at 3.3V level. Since your microcontroller is using 5V level, you should not do this but connect VCCIO to VCC (which is 5V).