Whilst you can't play FLAC you can convert to ALAC. However if you are going to the trouble of conversion for a portable audio device why don't you think about converting to high bit rate (>192k) MP3 or AAC in order to conserve space. I imagine lossless ALAC would take up much more precious iPod memory space for questionable improvement in sound quality if you are using the standard headphone output or Airplay?
I maintain 2 libraries ... one is FLAC for my hifi and the other is MP3 for my phone/portable audio. It's very easy to convert from the original FLAC using software like Foobar 2000, and if you have a large library, just set you computer to do it overnight while you sleep.