If you have problems with multiple connections per user, just limit the number of connections per ip/user, theres probably people doing that you miss now and again, why allow it, any decent ftp server will let you do it and set different rules for users or groups. Typically the rules of the internet are if it can be abused it will be abused.
I think download managers are better if they aren't abused on ftp servers that allow abuse, since they have recovery options , IE doesn't, flashget has automatic alternative mirrors to help spread the load, and it can be throttled , IE can't.
the throttling and limiting can all be enforced by the ftp server , but they certainly can't in IE.
I've also found that since it alwas puts it into a downloaded sorted folder for me, i can find the thing i downloaded easier, previously i would redownload a file rather than search for it locally
Also a vote for flashget i think its great.