I'm sure the U.S. military credited the explosion to a nuclear plant or something. Also, there's no evidence that Weyland Corp knew nothing about Peter's plans. Though the public may have been deceived, I find it very unlikely that a medpod and other advanced medical equipment went "missing" or was otherwise delegated and the company never even bothered to ask questions why such advanced technology was needed on an archeological expedition. As the Dark Horse Comics proved, there was sufficient data on the Prometheus mission and Peter's trip to it to attract snooping noses.