Basically, the shields they used would only block things with at least a certain threshold of energy or speed.

From the [Wookiepedia entry on shields][1]:

>The Gungan shields used during the Battle of Naboo blocked lasers, but droids could pass through because of their relatively slow movement in comparison to the laser bolts. 


  [1]: http://starwars.wikia.com/wiki/Deflector_shield