I've used atom since it was open sourced and really like many of the features it offers. But there is an issue with the mouse cursor disappearing when hitting the ALT key described here https://github.com/atom/atom/issues/2122 and the launch problem https://github.com/atom/atom/issues/3190

I've never used a .desktop file for atom and had no problems launching it until a recent update from the master repo. Guess I'll try installing the PPA package to see if that works.