Here is a hassle free way to create encrypted backup archives of your files upload them to a FTP server from the command line.
ZIPEncryptFTP is a C# command-line program that will let you create encrypted backups of your data without having to use a GUI and upload it to a FTP server.
To backup data with ZIPEncryptFTP just run this command from your command line
ZIPEncryptFTP /directory /password /url /ftpuser /ftppassword
Running the command will compress the files and sub-folders in the folder you specify to a ZIP file, encrypt the ZIP file using AES with the password secret your prove and upload the file to the FTP server, everything is done in the memory and it does not create any temporary files.
The software allows you to backup more than one directory at a time along with several other options.
To run this program you will require to have the .Net 2.0 framework runtime.