Unfortunately, no. The FTPit Pro Server Edition plug-in will only allow you to upload files from the FileMaker Server machine to an FTP server or download files from an FTP server to the FileMaker Server. There is not a way to upload a file from the end user's web browser (e.g. from Instant Web Publishing or Custom Web Publishing) directly to an FTP server using a FileMaker Server plug-in.

You could possibly use a web server side scripting language, like PHP, to upload the file from the end user's web browser to the FileMaker Server machine. Once the file was on the FileMaker Server machine, you could use the Server Edition plug-in to upload it to the FTP server.