I am not sure about why so many people are surprised. Although GitHub promotes open source, it's not open source itself. And it's fine. At the end of the day, GitHub is a company. They need money to do the great things it does.
While Open Source is great and it's contribution to the world is amazing, we shouldn't forget that it's a small niche thing, if we are talking about % of programmers contributing.
I interpreted "hackable" in this context to mean "personally customizable". Even if it's closed-source, that doesn't preclude an extension/library ecosystem from forming around the core Atom app, does it?
Except we would all be stupid to invest a lot of effort into said ecosystem when Github can pull the rug out from under it at any time, and Github will be the only one monetizing it.
Those of us who've been around longer have seen this play out many times. Free software isn't just dogma, it's very practical self-defense.
"They need money." Who doesn't? But it does not immediately follow that a software has to be restrictively licensed. It has to be part of an overall strategy. Most Open Source contributions actually come from companies pursuing a money making strategy. In the case of GitHub very successful even!
Equating open source to "not for profit" is just a misunderstanding of both business and open source. One of the main reasons for businesses contributing open source is a solution for the problem of the necessity of in-house development and the un-necessity of an unprofitable/risky in-house software marketing effort with all the overhead that entails.
While Open Source is great and it's contribution to the world is amazing, we shouldn't forget that it's a small niche thing, if we are talking about % of programmers contributing.