You can't really apologize for something that you, directly, didn't do. You can express how wrong it is to 'force' your views on another person. That people tried to 'force' their views on other people in the past, is a regrettable and wrong thing to do. I think you could say that much. I will say that much.
The Crusades were not about forcing view X on person Y. They were, like any war, about killing people and breaking things. But neither forcing views or killing people is necessarily wrong. I don't think the Crusades were wrong, they were overall a just, defensive war.
It is clear that war crimes were committed by the crusaders in that context. Some were committed as a result of poor individual judgement and others as a result of poor leadership. The sack of Constantinople, for example, was a colossal failure of leadership.
Those crimes need to be seen in the legal context of the rules of war at the time. Reprisals against the civilians are a war crime today. I don't know if the rules of war permitted them in 1099. I don't know if the natural law also universally condemns the reprisals. Consider that if the cause of the war is just, then the besieged citizens ought to recognize that, overthrow or at least passively resist the combatants purportedly fighting on their side, and open the gates to the invading army. To put it differently, in a siege environment, where the weapon is hunger, it may be impossible under natural law to separate combatants from civilians; such separation may only we available if the mutually understood rules of war codify it.
Since none of us participated in person, what would the meaning of an apology be? I think that if a fault is found, the apology is very meaningful if it comes from the same entity that initiated the behavior at fault. That would, in this case, be the Church Militant represented by the Pope in Rome, the same thing in 11 century and today.