Boeing is using new materials, and the new high-bypass engines for the 787 and 747-8 are quite a technological achievement.
People also forget that Boeing like many other aerospace companies rely on government funding and military contracts.
Many of Boeing's commercial aircraft either started as military designs for long range bombers and cargo aircraft or were a sister project of one.
Airbus was pretty much a hail mary effort by Europe to revive their aerospace industry, the UK, France, Italy and Germany have dumped billions of tax payer money to get Airbus off the ground. Airbus got preferential treatment in the EU market, and even it relies quite heavily on it's military wing for a large part of their profits.
As far as individual programs go the 787 like the 777 doesn't have military variants at this point, the "newest" Boeing aircraft with military versions is the 767 (there are plenty of 737 tankers and CIC/AW aircraft out there, and even 707's) and it does't look like they will ever receive one.
But it's also very hard to estimate the worth of a program, the 787 might not break even in the books, but the technology, experience, patents and intellectual property that came out of that program may very well be highly profitable.