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or they lost radar contact

Radar contact was not lost until it impacted the pentagon. You can't make a commercial jet invisible to radar, it's not a stealth plane. The part people get mixed up is the transponder was turned off, so people on the grould no longer had the insturmentation readouts or the call sign of the plane. And again, a lot of people were watching the radar data by that time, scattered all around the US.

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As far as I know, no one has ever really come out to say it's not true.

So that makes it true? Does the fact that Apple doesn't publicially dismiss rumors of a dual CPU colored Powerbook make that true?

There is enough evidence from when it happened to prove that flight 77 hit the Pentagon. They recovered 99% of the bodies, both black boxes, and tons of other commercial airliner pieces from the Pentagon.

A decent computer simulation done by an independant group is here. Much more scientific, and no attention grabbing music to try to make you believe some nonsense.