For me it's compatibility/convenience...
TrueCrypt has many advantages, especially its Linux support and absentee price tag. However, Cryptainer is more convenient for me to use, particularly since:
1.) It has a PPC/WindowsMobile version.
2.) Cryptainer Mobile has been simpler and more reliable than TrueCrypt's "traveller mode," particularly when administrative limitations were imposed on the machine being used.
3.) The ability to send self-decrypting e-mail attachments is a nice touch instead of having to tell the recipient another program must be installed for the contents to be accessible.
I'd love to see TrueCrypt's 'plausible deniability' touches added, but for the time being Cryptainer is just the best match for my needs.