Here's a link to a list of FTP programs NOT to use:
http://blog.unmaskparasites.com/2009...dentials-from/
The reason is that some viruses are designed to steal the stored login credentials with the intent of infecting the websites.
The virus works in many ways.
First, it looks for the file that stores the plain text login credentials. When it finds that, it reads it and sends the information to a server which then logs in with valid credentials, downloads either the entire website or just certain files, injects their malscript and then uploads back to the website. In the case many of the programs mentioned in this thread are only protected if you never get a virus.
So if you use a program like WS_FTP by Ipswitch, you're safe. Many of the others - you are not. Even using SFTP or FTPS won't help you much because the hackers can use those protocols too - with valid credentials.
Second, the virus works by "sniffing" the outgoing traffic. Since FTP transmits all data in plain text, even the username and password, it's easy for the virus to "see" the login data, steal it, etc. I created a video on this:
http://www.youtube.com/watch?v=oYI1kssrrbc
In this instance SFTP, SCP or FTPS will protect you because they send encrypted traffic.
Another way the virus works is by acting as a keyboard logger. This is to address those who say they never store their login credentials. Again, this particular case, it won't matter which program or protocal you're using, if you type in the login information, it will steal it.
The last way, we've seen, that the virus works is by injecting the malscript into the outgoing traffic as it leaves your PC. This one was interesting. The file on the PC is clean. As it's sent via FTP to the website, by the time it gets to the website, it's infected. This can only happen with FTP not the other encrypted protocols.
So there you have it. Want to know which FTP programs not to buy? Read the list at the first link.