The problem is in people's heads, not the sky.
Doubt is reasonable, there's no problem here. Unquestioned belief in "common sense" and what authority figures say is not. A lot of people have a lot to gain by leading the public to believe certain things. Isn't it too naive to assume that you are always being told the truth, when some stakes are so high?
If it were a single national airline, or even a subset of airlines, then maybe there would be cause for concern. But, a global conspiracy involving airlines, private airplanes, multiple governments, and tens of thousands of employees? That is patently ridiculous. Has anything on that scale ever been kept secret for long?
It may fail your 'for so long test' - could you define how 'so long ' is?
As your link points out, "By 1943, it was clear that the Soviet Union was attempting to penetrate the project". That was a year after the project started. http://www.mphpa.org/history/espionage lists "eight major spies who revealed secrets of the Manhattan Project." It wasn't a secret from the Soviets for very long.
John W. Raper published an article about Los Alamos in the Cleveland Press in 1944: 'Forbidden City - Uncle Sam’s Mystery Town Directed by “2nd Einstein”'. http://blog.nuclearsecrecy.com/2013/09/20/worst-manhattan-pr... . That was two years after the project started.
It was an open secret in D.C. It did, after all, require a huge number of people and money. As http://blog.nuclearsecrecy.com/2013/03/29/narratives-of-manh... points out, the mystique of secrecy around the project is different than the actual secrecy. Quoting it:
> "In the 1940s there was something of a small industry of articles, books, and clichés regarding how secret the atomic bomb was kept. Of course, the irony is… it wasn’t really kept all that well, if you consider “keeping the secret” to involve “not letting the Soviet Union know pretty much everything about the atomic bomb.” (Which was, according to General Groves, one of the goals.)"
So, the Manhattan project was secret for about two years, under its own operational goals of what "secrecy" meant.
It was public to the world by 1945, after the bombs were first used, so no more than a few years of secrecy under that standard.
The Soviet atomic bomb was in 1949, so still less than 10 years.
Anyway - who said it has to be "all airlines"? Does it have to be 1 vs all? Couldn't it just be some percentage?
In Operation Mockingbird [1], the CIA found that infiltrating just 25% of media outlets was enough to sway public opinion. That's the type of operation that is obviously still ongoing too.