Yes, Dimir Doppelganger's ability can target Chameleon Colossus while it's in the graveyard, despite protection from black. This is because in general, a card's abilities such as protection from black don't work while the card is in the graveyard (C.R. 113.6; review C.R. 702.16). (There are exceptions to this rule, but protection abilities aren't covered by the exceptions [review subrules of C.R. 113.6].) See also this thread, this thread, and this thread.
Protection and Copy