And yet in Assassin's Creed, the civilians and public agitators speak of the crusaders with fear, as though they were a terrible force, looming at their very doorsteps.
Seconded to what was said above, but also remember that you should take everything in Assassin's Creed's with a grain of salt. I'm glad I finally get to rant about this.
I haven't played Assassin's Creed, but knowing how the game works and what it's about lets me know that whoever designed has little understanding about the Assassins.
In the first place, and this pertains to your question, Assassins did not actually target Crusaders. The Assassins were a powerful political entity, but in the Holy Land they mainly stuck to Islamic targets. This is for a few reasons. One, they were already constantly in a struggle against orthodox Islam (the Assassins were Shiahs). Two, instead of seeing Christian invaders as the common enemy, the Assassins actually saw orthodox Islam as the common enemy.
The Assassins often made alliances with the Crusaders, taking commissions from Richard the Lionheart, treaties with Baldwin II, and several times trying to murder Saladin.
In the second place,
one Assassin carrying out nine assassination, or even more than one or two, is not realistic or how the Assassins operated. Despite what you may get from Assassin's Creed, or even read on Wikipedia, but the Assassins were not a group of highly-trained, professional, ninja-like assassins. They were actually a group of highly indoctrinated fanatics, who typically "went down with the ship". They were trained enough to murder a target, but were not expected to return.
They were actually a dangerous religious sect whose power was built more around fear than actual ability to assassinate. Many assassinations flat out failed (including the many attempts on Saladin). A large source of their power came from the fear and awareness that seventy thousand followers were willing to kill, or die, at the drop of a hat.
So that was Assassin's Creed for how it pertains to the actual Assassins. Regarding civilian's fear of Crusaders, I agree that civilians scarcely appreciate any kind of foreign military presence.