You get hexagons because of close-packing.[1] Circles (or a 2D array of spheres) of the same size fit closest together when they are arranged in a hexagonal pattern. Push a bunch of marbles together and that's what you get. The bees don't know anything about hexagons. They just make circles close together and then as the cells are filled, stepped on, and come into contact with other wax cells, they "ballon out" into…
Is this the generally accepted explanation now? (I thought so, but the article itself doesn't mention it - then again, the article seems full of pseudo-science)
[1] http://www.localhoney.co.uk/wp-content/uploads/2010/06/start...
[2] http://1.bp.blogspot.com/-uM7ATVMEcDA/TdcWZm9BPEI/AAAAAAAAI8...