The short answer is that it seems to be standard policy for Starfleet personnel to transport with both hands free, facing the front of the transporter. There are a few instances in Enterprise, Voyager and TNG where they beam into hostile situations with their phasers drawn or standing in a circle (or both) but these are very much the exception rather than the rule.
TNG : Legacy TOS: Day of the Dove
As to why they keep their weapons drawn, the Star Trek : Deep Space Nine - Technical Manual seems to suggest that it's a question of transport efficiency to keep everything directly above a single pad.
