FileZilla is an FTP application. Its weakness is that it stores passwords in plain text, so is vulnerable to trojan attacks on your computer.
WinSCP isn't a magic pill. Nor is WSFTP. But they don't store passwords in plain text, so don't have the vulnerability that FileZilla has.
That said, if YOU tell ANY program to use plain old "FTP" protocol when talking to a webserver/ftpserver, YOU will be passing YOUR passwords AND all your data in plain text, unencrypted.
To overcome that, you need to arrange for using a secure FTP method, such as SFTP or SCP/SSH or FTP-with-implicit-SSL etc, with your hosting company so that you can transmit your data in a manner that encrypts/protects all the data you exchange between your PC and the server.
Just like using SSL on pages that collect passwords or personal or financial/creditcard information.
You can read up all about all these concepts using your favorite search engine and probably wikipedia etc. If your hosting company doesn't know what you're talking about, find one that does before you spend any money with them.
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