The rules for "protection from [quality]" are the same regardless of what quality it is (C.R. 702.16a-f; under C.R. 702.16a, that "quality is usually a color ... but can be any characteristic value or information"). Even if Beloved Chaplain had protection from green (or from another color), rather than protection from creatures, that doesn't mean any Auras attached to Beloved Chaplain also have protection from that quality — among other things, those Auras can be targeted by spells of that color and by abilities from sources of that color as normal (review C.R. 702.16b).
EDIT (Jul. 19): The cited text was slightly added to in Core Set 2019.
The specific example..."illuminated wings" enchant creature on a "beloved chaplain" (1/1 w/ protection from creatures).
Opponent uses Viridian Zealot to destroy the enchantment.
Is that a good play? Been a while since I played and forgot some things along the way. Thanks.
Awesome avatar provided by Krashbot @ [Epic Graphics].
EDIT (Jul. 19): The cited text was slightly added to in Core Set 2019.