The interaction between trample and protection has changed over the
  course of the game.  Nowadays, it's as follows:

  Combat damage happens in two distinct steps, assignment and dealing.
  In assignment, an object is put on the stack that records the source,
  destination and amount of each piece of combat damage.  If a creature
  has trample, then it's legal to assign some or all of the damage from
  that creature to the defending player, as long as the assignment
  also assigns lethal damage to all creatures blocking the creature
  with trample.  Lethal damage is considered as however much damage is
  needed to make up the difference between damage already on the creature
  from before the assignment was made, and the toughness of the creature.
  Effects that would alter the amount of damage that actually gets dealt
  are not taken into account at this stage.

  When the damage is dealt, there may be replacements that alter the
  amount of damage or prevent it entirely.  This is where the protection
  can step in and shield the creature.

Some parts © 2009 Advameg, Inc.