One thing that always bugged me about this otherwise great FTP application was that it didn't show hidden files on the server, such as .htaccess. There was no obvious setting to enable it either. However, thanks to some help from this page I've found out how you do it. Start the program and when the connection dialog (where you choose which site to connect to) appears click on Start Up. Then in the remote file mask box put in -a
It's that simple!