The Belmont Club did an analysis, and isn't sure.
http://fallbackbelmont.blogspot.com/2005/09/flight-93-memorial.html
Actually, they found that all data seemed to correspond to the memorial being aligned toward Mecca. It was the crescent design which they thought might be a coincidence. The website the Club examined (that of architect Nelson Byrd Woltz) had nothing to do with the design... And, at any rate, the use of a crescent shape, while an oft-repeated design through history, has absolutely no place at the crash site of Flight 93. Any high-school senior could tell you why.
The placement, and the design, was deliberate.