Flight sim is excellent for getting practice in intercepting and tracking to and from a VOR or NDB. Once you can do that (intercepting a track to or from an NDB is not child's play, especially not with wind and of course you can set your own wind in FS) you can progress to holds and approaches.
Set all the realism settings high (not the display ones but the ones to do with gyro forces, gyro drift &c.) and get to know the wx settings properly so you can set your own cloud base and vis.
I think MS FS saved me at least £200 worth of flying in the early stages, getting the hang of NDB tracking (+30 aiming for -30 and all that), NDB holds, &c. I still use it to fly new procedures if they look complicated or unusual before I do them for real.
Tim