A lot of the discussion above is whether military spending gives Boeing a covert subsidy (and it must have given that to Lockheed, who would otherwise have been bankrupted long ago by their various civil programmes over the years).
But a further source of R&D funds that Boeing can draw on is NASA. While the US public think their funds are going to the space shuttle and the next moonshot, NASA in fact does a tremendous amount of aviation research which US manufacturers can draw on, and in fact often co-operate with (because it saves them doing it, of course). Sure, much of it is good stuff, but it's another subsidy to the US side.