You will find +'s and -'s about both, but generally a Micro Drive hard disk isn't as safe if you drop it as a compact flash is which has no moving parts.
Just image dropping the hard drive of your computer and see how that fairs. Generally not well, if not completely dead as the heads would either be damaged, end up miss aligned, or the platerns would be marked in some way. Not to say that it might not still work.
Compact Flash are generally faster write/read speeds than the hard drive, which takes time to spin up and down looking for the files.
I think if you did a poll, you would find that a vast majority of people use Compact Flash over Micro Drives, as they are generally shock proof, can take a dunking in water accidentally (need to be completely dried out) and the good ones have life time warranties as well.
Hope that helps.