In both games, Altaïr is used as a symbol for everything that the Assassins represent: he is atheistic, driven by rationality and curiosity and he is faithless, which is not to say that he doesn't trust anything but that he doesn't trust anything unknown. Throughout the game, his leader Al Mualim tries to convince him of the dangers of knowledge. He commands Altaïr to kill, expecting him to follow without question. But to Altaïr, a true Assassin who uses reason and logic to determine what is best for the common good, the denial of knowledge is practically heresy. So it is not surprising that Altaïr continues to question his master even after being warned not to. This questioning is eventually rewarded when Al Mualim is exposed as a Templar in disguise. Whereas most of the Assassin's have blind faith in their master, Altaïr does not. The game discourages blind faith in anything, even one's own leaders, a theme defined in the Assassin's creed itself: nothing is true, everything is permitted.
While the first part of this creed seems more nihilistic than anything else, the Assassin's rejection of "truth" is perhaps better expressed as a rejection of blind faith. The Assassins are a humanistic society, and as such, they don't accept as true anything that they haven't seen for themselves and even then they understand that truth can be manipulated. The phrase is meant as an acknowledgment that no one person can know everything; it is meant to humble the speaker and encourage an open mind. The second part of the creed describes the means with which they should uphold this ideology: everything is permitted. Their belief in the common good trumps any law by the current government; they are assassins after all. But it's interesting that this group of people so intent on the common good would flaunt the law so uncaringly. They're essentially vigilantes, breaking the law to uphold justice like any good superhero. That's why players are so willing to believe that this group of atheistic killers (traits normally associated with immorality) are the good guys. Despite their background they act like your typical hero.
