First of all, this is a BAD Idea. Apple Considers this an OS folder and so we also consider it as such.
A better way to do this is to use the folders that are already supplied for user programs. Or to create your own folder and add it to the path (Environment variable). This way you can run any of the programs form anywhere you are in the folder structure, and the folder will be selectable from the standard list of folders.
That said, I did set up a rule to backup the /usr/local/bin.
I set the Backup up files inside: to the Mac Hard Drive. Then I set the rule to any parent folder is usr/local/bin.
I had it set to /usr/local/bin but the initial "/" was removed.
This worked just fine and backed up files from the /usr/local/bin location.
You can also use the following command to "unhide" this and many other files/folders from the finder.
In the terminal, paste/type the following line (Note: USE AT YOUR OWN RISK)