As already said by bigstar FlashFXP runs well under Wine. I have used it a lot and it doesn't give me any more grief that most other GUI FTP clients do in Linux - my only problems were with icons and other minor cosmetic stuff.
As for SSL-support, look into lftp. While "just" a command line interface client, it's incredibly powerful and easy to use. Nowadays it's the only FTP client I use in Linux.
If you don't like lftp there's always the plain old "ftp" client with Kerberos and SSL extensions from KTH.
hw_tph
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