That's because damage does not reduce toughness. The -2/-2 from your Massacre Wurm made the still 3/3 Doctor Doom into a 1/1. He had 3 damage marked, which gets compared by state based actions against his toughness to determine if that damage is lethal. And it is. But being indestructible with a toughness higher than 0 means he lives, because that specific state based action destroys. A different state based action can kill an indestructible creature, because it is not destruction, but it requires the tougness to actually be brought down to 0 or less. You can't combine damage and toughness reduction to remove an indestructible creature, it has to be toughnes reduction all the way.

Here are the two relevant rules/state based actions:

704.5f If a creature has toughness 0 or less, it’s put into its owner’s graveyard. Regeneration can’t
replace this event.

704.5g If a creature has toughness greater than 0, it has damage marked on it, and the total damage
marked on it is greater than or equal to its toughness, that creature has been dealt lethal damage
and is destroyed. Regeneration can replace this event.