"Destroy all creatures" destroys my indestructible creatures
Cards that say "destroy all creatures" consistently destroy my indestructible cards like Heliod, Sun Crowned. They end up in the graveyard. By definition that should not happen.
Also, Protection from Color does not allow a creature to survive "Destroy all creatures" cards.

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[Deleted User] commented
Don't know about the first part without knowing what was used and what was on the field at the time.
As for the protection part, "destroy all [...]" does nothing that protection can protect against. Protection only does four very specific things. Remember them by DEBT:
D amage is prevented
E nchanting/equipping is not possible
B locking is not possible
T argeting is not possibleSo protection can help against damage based mass removal like Blasphemous Act, but not against simple "destroy all" effects like Depopulate.