I installed an application in this location /root/jython and I added a link to the /usr/bin because i want everyone on the system to be able to execute this
ln -s /root/jython/jython jython

I can execute this anywhere when i am logged in as root but when i change user to say juju it returns

juju@sus:~>jython
bash:jython: command not found

Well, you can check if the other user has privileges to read/execute the directory (/root) and the file.

But I would install the application on another place, like /opt, and then add to the PATH the binary directory. Installing applications into root's home directory it's not a good choice.

So, if you install the application on, let's say /opt/jython and the executable file is there, then you should do an export PATH=$PATH:/opt/jython:.

Good luck.