I don't think there's a huge difference between Boeing and Airbus when it comes to military/government R&D assistance. NASA's aeronautics budget is a joke. Boeing gets lots of military R&D money (including IRAD, or independent R&D, that's built into overhead on all contracts), but since Boeing Commercial does not think that the defense side has anything to teach them (they're wrong) this has little effect.
Launch aid is a big benefit to Airbus, but it's legal under the 1992 agreement. Boeing also benefited massively through the 1990s from an export tax break that the Europeans complained about, until it was removed.
Meanwhile, Boeing is getting big-time money related to 7E7, including up to $3.2 billion from Washington state and an undefined amount from the Japanese government. Boeing ties itself in knots insisting that those aren't "subsidies" but they look a lot more like that than the relatively small tax breaks that Airbus has received (for example) because of its expansion in North Wales.
Also, the Boeing tanker deal was initially set up by Congress to help Boeing, post 9/11. Noncompetitive, and it would have helped cover overhead on Everett - which otherwise is becoming a one-aircraft plant - and keep the excellent but expensive 777 in the game.