In that case, keep your changes and improvements in your own branch, and don't submit a pull request for them. If you don't want to share it for "free," that's your call.
well, its not "your" code is it? GitHub have written it. If you don't want them to profit off your work, don't submit patches to Atom?
The whole point is they're trying to have it both ways. They want to benefit from other people's work freely (that's why they're accepting pull requests), but do not want to let others benefit from their work in the same way.