I have to maintain an FTP server that provides about 14 different kind of things. It's hard to explain, and pretty boring to boot. The FTP server I use is running on Linux because I needed to isolate it from the rest of my Windows Server 2003 network. The Linux machine does such an amazing job. I put this server together for less than $800 and then put a free operating system on it and it is screaming fast, super reliable and unbelievably flexible. I happen to use Fedora Core Linux and vsftpd (Very Secure FTP Daemon,) but there are other Linux FTP server combinations that would work as well.
There is one Windows development server that I have had to keep FTP running as part of the development work. Yikes! What a problem that is. I get 70,000 attempts to login as administrator. That's not a good thing. Hackers find out that it's a Microsoft FTP server and the attacks begin. They figure if they can get the administrator user, it is really the administrator user for the entire network. That would be bad, folks. Very bad. So, I have to keep that development server under very tight wraps from an IP address range standpoint. That's yucky. I would not want to have a truly public FTP server running Microsoft IIS. Maybe anonymous only access, but nothing that would require logins.
I have had people try to get the administrator password via FTP on the Linux box. I just laugh at them and smirk mightily at their expense. There is no administrator password for that server. Even if they did find a password to a user that did work, chances are that it really only exists for FTP, because I use all virtual users for FTP. There are only five or six real users on the Linux box, and none of them are the same as the users for Windows network.
As with most things Linux, you have to be committed to a fairly big learning curve on setup and configuration. When it comes to services like FTP, Linux really wants you to know what you are doing. You can get something functional, without knowing a whole lot, but you won't get the flexibility nor the performance without delving into the crazy world of config files and scripts.
The Windows FTP server does set up pretty darn easy, and you can maintain it with just the basics in knowledge. The price for that is some security issues and reduced flexibility. You have to do it the Microsoft way - which is miles more flexible than the Apple way. Don't get me going on that! With Microsoft, there is usually some flexibilty. With Apple, it's Steve Jobs' way and you better like it, too - or you're out of the cult and they'll send the Apple Thought Police after you.
Sorry. I'm back now.
So, if you have to set up an FTP server for a single purpose and you know exactly who is going to be using that server, the Microsoft FTP server in IIS could be OK. But not really. If you have any special needs, or you have multiple sites or you need to have FTP-only users, spend the time, but not the money, to move up to Linux. You will be happy you did.
Winner: Linux, by a knockout. Not even close.
