Thanks to @AndrewThompson
Quote from wikipedia
As a powerful religious symbol, the burning bush represents many
things to Jews, Christians and Muslims such as God's miraculous
energy, sacred light, illumination, and the burning heart of purity,
love and clarity. From a human standpoint, it also represents Moses'
reverence and fear before the divine presence.
Throughout the movie, Balian was eager to find God and actually talk to him. He travelled from France to Jerusalem to do so, and in Jerusalem he did not find anything different. Hospitaller then tells him that holiness is in right action and protecting the ones that need help. Balian, still not able to talk to god doubts his presence and here lets off a rant about God and if he actually exists, since the fire from the burning bush apparantly dictates God's miraculous energy. Hospitaller replies that it does not mean that God does not exist.
Later in the Movie, Balian knowing that actually physically or mentally talking to God is impossible and when he is about to burn dead bodies to save the people, he says something along the lines of "If God does not understand this, then we need not worry since he is not God.
You can see later from the scene that the bush actually does not burn, instead just dislocates from its root and another flame starts up, indicating to Balian that God may do really exist.