Toward the middle of the novel Alyosha is directly identified as the "hero of the novel" by the narrator.
Perhaps more significantly, as the philosophical opposition is developed between faith and disbelief in the novel, the preferred existential position is clearly established. Faith is the position of virtue and disbelief leads to chaos, betrayal, crime and evil.
Early in the novel this is conclusion is neither clear nor foreshadowed and only becomes clear finally when Ivan faces the devil in his delusion-driven nightmare. Ivan ultimately represents the inevitable despair born out of disbelief and human pride which the novel is so interested in exploring and, in the end, condemning.
Alyosha represents the opposite side of this existential and philosophical divide, literally characterizing the virtues of faith and constantly rescuing others through this honest, humble faith.
Alyosha is the hero of the novel because he represents the winning side of the novel's central argument regarding which position is best for mankind - to humbly believe and trust or to push forward to a man-made revolution, doomed to failure because of the weakness of men.
There are passages in the novel which do suggest that Dostoyevsky is open to considering (and maybe believing in) the potential benefits of atheism and in the socialism attached to it in the novel. However, the idea of a Russian-Christian revolution wins out in The Brothers Karamazov.