If the controller of the creature with trample wants it to, then yes. Trample works by letting a creature just assign lethal damage to the creature it is blocking, and it may assign the rest to the player, but doesn't have to. Trample doesn't care what will happen when the damage is dealt, so even if a creature has protection, trample damage can still go through.
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"If you knew anything about the lore you'd see that they were clearly hinting that the madness on Innistrad was caused by Uncle Istvan wearing Urza's Power Armor ... tainted with Phrexyian Oil"
Graham from Loading Ready Run
...which happens to be the very same example provided in the rulebook, had you bothered looking:
702.19b The controller of an attacking creature with trample first assigns damage to the creature(s) blocking it. (...)
Example: A 6/6 green creature with trample is blocked by a 2/2 creature with protection from green. The attacking creature’s controller must assign at least 2 damage to the blocker, even though that damage will be prevented by the blocker’s protection ability. The attacking creature’s controller can divide the rest of the damage as he or she chooses between the blocking creature and the defending player.
so if a creature with trample is blocked by a creature with protection from their colour, does the extra damage go through?
Graham from Loading Ready Run
702.19b The controller of an attacking creature with trample first assigns damage to the creature(s) blocking it. (...)
Example: A 6/6 green creature with trample is blocked by a 2/2 creature with protection from green. The attacking creature’s controller must assign at least 2 damage to the blocker, even though that damage will be prevented by the blocker’s protection ability. The attacking creature’s controller can divide the rest of the damage as he or she chooses between the blocking creature and the defending player.
http://magic.wizards.com/en/gameinfo/gameplay/formats/comprehensiverules
RULES OF MAGIC :
http://magic.wizards.com/en/game-info/gameplay/rules-and-formats/rules