It appears from their website that Free Download Manager simply starts at the index file and then follows all links.
There are a lot of programs that do that.
Since it's using ordinary http to get the files, and following links, it's doing exactly what a web browser does.
I suppose you could write a proxy for, or rewrite, apache, to not allow connections from a server sending the specific header information that Free Download Manager sends.
Would you do this for wget, and the dozens of other programs that do the same thing?
Jeff