Why was the manhattan project kept so secret?

Many people working on it didn't actually know what the project was. They were only working on a small portion of it and were not told that it was an atomic bomb they were working on (as if they'd have known what that was, since there wasn't one yet).

Throw in the very tight and heavy security on it, both military and secret service, and the fact that government had tight control over communications going in and out of the labs (even heavier than the Patriot Act), and there is no reason to doubt that it was kept fairly secret.

9/11 Troofers are claiming things that just did not happen and doing so in direct opposition to the vast amount of proof and evidence that directly contradicts their claims.

It's different. Very different. Conspiracy theories are intellectual discontinuities.