Atta, in short, never did anything for pleasure. So his two trips to Prague in May/June 2000 just before he entered the US for the first time are very significant. As any transatlantic flier can tell you, it is far cheaper to fly from Germany than it is from Prague. And yet Atta goes out of his way to fly to Prague first. And then, when they won't let him in, he returns to Germany, obtains the proper visa, and takes a bus to Prague just to ensure that he gets there. Whatever it was, it was extremely important to Atta. And Prague is not known for any significant Al-Qaeda presence. It is known for its Iraqi diplomatic presence.
..one senior U.S. law-enforcement official tells Newsweek
What, do you doubt the word of these unnamed senior law-enforcement and intelligence officials!!??
Next, you'll even be doubting the FBI!
Instructions or guidance could have been sent by email or telephone or courier.
His trip to Prague was a risk: he may have been denied re-entry into the USA.
Why was it so absolutely important to Atta that he get to Prague IN PERSON?
The only logical answer I can see is to pick something up, something small that he could carry back to the US, something that was too valuable to be entrusted to a courier.
A small disguised flask of anthrax spores is my guess.
(As an aside, and sign of the times, the day Atta re-entered the US on his expired student visa, Tenet was at CIA HQ celebrating "Gay Employee Appreciation Day", I kid you not.)