Well, one can only assume, based on the wording they use here:

https://github.com/atom/welcome/blob/master/lib/welcome.md

> Atom is free during the beta period.

Atom won't be closed source, but it won't be open source either. It will be somewhere inbetween, making it easy for us to charge for Atom while still making the source available under a restrictive license so you can see how everything works. We haven't finalized exactly how this will work yet. We will have full details ready for the official launch.

> http://discuss.atom.io/t/why-is-atom-closed-source/82/9