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**  
![enter image description here][1]

As to why they keep their weapons drawn, the [Star Trek : Deep Space Nine - Technical Manual][2] seems to suggest that it's a question of *transport efficiency* to keep everything directly above a single pad.

![enter image description here][3] 


  [1]: https://i.sstatic.net/sN6sV.gif
  [2]: http://en.memory-alpha.org/wiki/Star_Trek:_Deep_Space_Nine_Technical_Manual
  [3]: https://i.sstatic.net/0iOfg.png