I tried it myself and it worked perfectly, even after a reboot. Do you have multiple disks/partitions in you set up?
Anyway, to settle things once and for all, I suggest you to follow the steps pointed out here. Below is a copy&paste.
With the Atom editor open, in the menu bar:
Click Atom >> Install Shell Commands
You should expect to see:
You do not need to restart the terminal.
If this solution didn't work, my last suggestion is to create an alias in your
~/.bash_profile. To do this, simply open
~/.bash_profile with a text editor and add somewhere the line:
alias atom='open -a Atom'
This should do the trick.
I noticed that after a reboot, you must start Atom at least once before the
atom command works - otherwise it won't be recognized as a command. I didn't notice it before because, while testing if the
ln -s ... solution worked, I already opened Atom once. I honestly don't have a clue why this happens, but the last suggestion about adding an alias definitely solves this issue.