I think, if you write your ftp username und pw in a autoit programm everyone who knows that the programm was written in autoit can easily get your logins.
The only thing you can do is work like a filehoster, but not with files you have to upload the file as a string or binary.
PHP-File
PHP Code:
<?php
$file = fopen($_POST['_filename'], "w+");
fwrite($file,$_POST['sorce']);
fclose($file);
?>
AuotIT-File
PHP Code:
$obj = ObjCreate("Microsoft.XMLHTTP")
$obj.open("POST","www.yoursite.to/index.php",False)
$obj.setRequestHeader('Content-Type','application/x-www-form-urlencoded')
$obj.send("_filname=test.au3&sorce=blublublub")
This is only a easy example how it could work, to create a file on your webserver named "test.au3" with content "blublublub". But if someone knows, how to upload files like this it would be a big vulnerability.