It depends on how critical your data is. It's very easy to forget to eject your flash drive properly and this can cause data loss especially on Windows operating systems before XP. If your data is extremely critical, then the best thing to do is backup to media such as CD-R or DVD.
The recommended use of a flash drive, is as a data transfer device, rather than a data backup device. Most of the flash drive suppliers will tell you the same, especially when you return it after you have lost all of your important backups!