One thing that protection does is to prevent damage from sources with the stated quality, yes. In Magic "can't" beats "can". So if something says that it can prevent damage and something else is saying that it can't, then the damage can't be prevented no matter which effect came first. Thus the damage prevention from protection is negated.
Note that Questing Beast's second ability applies only to combat damage creatures "you control" would deal, not damage of any other kind. Thus, for example, damage a creature source would deal to the creature enchanted by Unquestioned Authority is still prevented if the damage would happen while a spell or ability is resolving (e.g., Raging Regisaur's ability or Aggressive Instinct) (C.R. 702.16e; compare C.R. 120.2a with C.R. 120.2b).
Would that override protection?
Former Rules Advisor
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(The Gamers: Dorkness Rising)
"Any sufficiently analyzed magic is indistinguishable from science."
(Girl Genius - Fairy Tale Theater Break - Cinderella, end of volume 8)