Tax breaks for companies are a subsidy. (Aside from the military cross-subsidisation.)
2. Having the government take less of your money is not a subsidy.
3. Boeing 2016 revenue was $95.5 billion. The tax break is about a quarter of a percent of that.
4. I'm curious what you consider military technology that makes up the 747.
5. I'm curious what part of the Everett plant, which was built from scratch to build the 747, was built with government/military funding.
Tax abatements are not subsidies.
Here's the rebuttal to your link:
http://www.boeing.com/company/key-orgs/government-operations...
In particular,
"The USG's defense against the charges noted that the NASA and DoD contracts in question were arms-length commercial transactions where Boeing was paid for research commissioned by the two government agencies. The USG further noted that the NASA research projects were undertaken for public benefit, and that the results and benefits were widely shared, including with Airbus."
Boeing lost money for the first 10 years on the 747, but then it started making massive amounts of money off of it. Those profits funded the 757, 767, etc.