Disclosure: Former Boeing Employee.
Some R&D examples I've seen is the movement of advanced electronics and structural materials from military craft to commercial craft. Boeing and AirBus both benefitted tremendously by their military contracts.
If you look at things like the Boeing/Northrop Grumman Tanker contract, then it is hard to fathom that any of the $35B for 180 planes (that's 190M for each plane) wouldn't lead to significant development that could be shared with Boeing's commercial sector.
The Boeing 737NG line is probably their most profitable product overall. That is from Boeing Commercial Aircraft.
Some financials for your reference [1] http://boeing.mediaroom.com/index.php?s=20295&item=128736
It does give you economies of scale in the sense that any larger company gains purchasing power and for that matter visibility (and political power) by employing more people.
The airlines were, for a long time, subsidized by air post. Fuel prices are still much lower than they could be.
These things are barely directly profitable, but they contribute immensely to the global economy. That's the interesting tradeoff in post-capitalism.