Hi Tim,
this really depends on where you fish, swim condition, target species and what the fish are feeding like on the day.
If you're after fish in a swim which has snags and you want the bait to trot or trundle through then bury the whole hook in the bait.
If you are legering and the bait will be stationery or float fishing either laying on, overdepth or up in the water (anything other that dead depth) then you can leave the point exposed.
I would rather leave the point showing in order to increase the chance of a good hookhold, it's all really down to the conditions on the day, many people (including myself when possible) use a hair rig leaving the whole hook free to do it's job.
Hope this helps.