Recently, an increasing number of people have started advising moving away from FileZilla. However, the only reason I can see for this is that FileZilla stores the connection information in a completely unencrypted form, but as Mozilla says - surely it is the job  of the operating system to protect the configuration files?

So, is there any other reason why I should no longer use FileZilla, as I've never had any problems with it? Somebody mentioned to me that the way it works isn't secure either, but I think they were just getting confused over the fact FTP transmits passwords in plain text anyway. 

FileZilla per se isn't inherently insecure. Yes, it's storing passwords in plaintext, but the alternatives are only slightly more secure. You see, encrypting the credentials requires an encryption key which needs to be stored somewhere. If a malware is running on your user account, they have as much access to what you (or any other application running at the same level) have. Meaning they will also have access to the encryption keys or the keys encrypting the encryption keys and so on.

Your best option here is to disable password storage in FileZilla



Then start using KeePass to store your account credentials. There are also many guides on the Internet about how to integrate KeePass with FileZilla. Doing this, you're storing the encryption key somewhere where malware don't have access; you're storing the encryption key (or rather, the password from which the encryption key is derived) in your brain.

Finally (and perhaps this is a bit outside the scope of your question), please make sure you move away from FTP in favor of SFTP.
