My speculation of the obvious: It’s going to take a lot longer to get a working build on Windows than on Linux.
Windows is really super-finicky about how it compiles things in node-gyp, and node’s reliance on that build system makes building the app on Windows harder.
Also, binding things to the UI is much more similar between the major Linux flavors and OS X (“Just use the window manager!” :-D), than it is between Windows and OS X. It’s gotten easier to build things for Windows in recent years, but it’s still apples-and-oranges with looking at it from the perspective of porting code from an OS X build.
The fact that they have a Windows build process working at all is impressive. But, don’t expect it until well after you see a Linux release, unless they dedicate a small team just to the Windows port. Given the bottom-of-the-hill status of Windows as a development platform*, I don’t really see that much in terms of resources being given to make Atom on Windows happen that quickly.
(* Also, most of the hardcore Windows development community are going to be using Visual Studio as their primary editor, regardless of the presence of other editors.)