from a technical/security standpoint i completely agree. however if you're not working with other people (and most people use ftp) then you're the one doing it wrong.
i don't know where you heard that but it is false. don't spread (mis)information before confirming it. i'm running latest filezilla (3.5.3) and just checked. its stored plaintext.
but tons of apps store sensitive info plaintext.. really its up to the user to make sure people aren't stealing their fucking files.