This doesn't mean that using wine is a bad idea. Precautions could be taken to jail the wine installation. For example, the wine package could be changed so that it created a new user, and all wine apps were run by that user, so that your windows apps wouldn't have permission to mess with your files specifically. People have talked about this on the wine mailing list before.
ANY Linux program could be trashing your home folder the same way a virus run under wine does, it's just that people tend to develop more data trashing programs for windows
Note that running the virus under wine is still more secure than windows -- it can only trash the things you as a user have permission to trash, so the most it can muck up is your home folder.
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