Cyberduck is a popular free FTP application for Mac OS X. As mentioned in a previous article Show hidden files on Mac OS X, you can use Cyberduck to view hidden files like .htaccess and others beginning with a period.
However, there are cases where Cyberduck does not show hidden files. This is a known issue in Cyberduck – it happens when servers do not send data about hidden files when using the STAT command. If all that technical-speak didn’t help you, ignore it 
The fix to show hidden files in Cyberduck is a single command in Terminal. You can open Terminal from Applications > Utilities > Terminal, or by typing the first few letters into Spotlight.
Enter the command below:
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defaults write ch.sudo.cyberduck ftp.sendStatListCommand false
If, for some reason, you need to revert this, simply replace false with true.