You don't say how you have in mind doing this. Something like PGPdisk or
WinXP Encrypting File System should work fine and relatively transparently.
Is it safe? That depends on the quality of the tool and your ability to
remember the passphrase. Is it preferred? To what? I think many more people
lose their Money data to lack of backups, corruption problems, inopportune
reformats/reinstalls, etc., than lose privacy of their data to computer
security problems and to people trying to exploit these problems for access
to other people's Money data files.