Both are owned by Boeing. If Boeing Military is growing fat on military contracts and subsidies,  it can carry it's commercial division if need be. Let's call that cross-subsidization. 
I have little doubt the US govt aids and abets the Military Division in this process, including strong arming allies to buy Boeing products. 
Nor would I be surprised to hear the US govt has ways of tilting the playing field in favour of the Commercial Division too. Oh wait, that's what this is all about in the first place.