When you activate a regen ability - say, by paying G for Cudgel Troll - what you're really doing is activating an invisible "regeneration shield" around that creature. This shield is a sort of contingency replacement effect.
The next time [this creature] would be destroyed this turn, the regeneration shield "pops" and replaces that event (the creature getting destroyed) with three things:
1) All damage marked on it is removed;
2) It's tapped;
3) If it's attacking or blocking, it's removed from combat.
What's important is that this is a replacement effect for when the creature would otherwise be destroyed. It's not 'healed', tapped and removed from combat simply because you activate the shield; those things only happen if it would be destroyed this turn (and it hasn't already used the shield up).
So simply blocking a creature with your Cudgel Troll and paying G to regen it won't remove it as a blocker. In order for it to be removed from combat, it has have lethal damage marked on it, which means your opponent will have to have assigned the appropriate damage to it. Not all of their damage will trample through.
If they find a way to destroy your creature after the regen shield is activated, but before combat damage is assigned, thus "popping" the shield and removing your creature from combat, then yes, all the trample damage will go through to you. But they have to have a way to destroy your creature before damage is assigned for that to work.
The "regeneration shield" doesn't kick in until the time the creature would actually be destroyed. That time is after damage as been assigned and dealt, which means the defending player would have already been assigned and dealt the appropriate amount of trample damage.
When a creature with Trample attacks and is blocked by a creature which can be regenerated, the creature can be regenerated, but regenerate does not prevent any damage done to that creature's controller from Trample. MagicWiki
Damage will still be dealt to the regenerated creature (enough to kill it), and it lives, but the rest will go through to your life.
Hope this helps.
Im still confused, in dotp 2013 one of the challenges opponent regenerates against my trample and then takes all the damage from it.
Mind that DotP does have bugs occasionally. Which event is it? What creatures are involved?
It was challenge stolen goods. There is no bug though. I attack, cudge troll blocks and regens then i use a kill spell so its all good.