Oh I see! It’s because the armature modifier takes one armature as an input while all of your bones are separate armatures. Quick fix is to select all your armatures, make the root the active object, and press Ctrl+J to join.
For more about working with armatures and bones, I would definitely recommend Wayne’s new rigging course:
https://cgcookie.com/course/fundamentals-of-rigging-in-blender-course
Hope that helps!
