• Base Answer : Yes both jews and muslims and Orthodox (with some minorities) were persecuted in the Christian Crusader States.
• Long One: Depending on the sources both (European - Middle Eastern) agreed that the Christian Crusaders massacred the Muslims and Jews directly after Siege of Jerusalem. European sources/Eye Witnessesone quote which is from Gesta Francorum : " "[Our leaders] also ordered all the Saracen dead to be cast outside because of the great stench, since the whole city was filled with their corpses; and so the living Saracens dragged the dead before the exits of the gates and arranged them in heaps, as if they were houses. No one ever saw or heard of such slaughter of pagan people, for funeral pyres were formed from them like pyramids, and no one knows their number except God alone. But Raymond caused the Emir and the others who were with him to be conducted to Ascalon, whole and unhurt." Arab sources give figures of between 30,000 and 70,000 casualties (in an anonymous Syrian chronicle, and in Ibn al-Athir, respectively). These figures are rejected as unrealistic by Thorau (2007), who argues it is very unlikely that the city at the time had a total population of this order; medieval chroniclers tend to substantially exaggerate both troop strength and casualty figures; they cannot be taken at face value naively, and it is less than straightforward to arrive at realistic estimates based on them. They might be true they might be just exaggerations. As of your question about being treated in later days. Well according to The impact of the Crusades on the Near East

by various writers they claim that minorities were in a different social class than Christians themselves.

• Edit : Saracen means Muslims/Arabs just to clarify