Jack's choir boys were outnumbered by the other kids on the island. Although "with dreary obedience the choir raised their hands" for Jack, the other boys all voted for Ralph. It was obvious to them that Jack's "simple arrogance" was not a quality of leadership.
... there was a stillness about Ralph as he sat that marked him out: there was his size and attractive appearance; and yet most obscurely, yet more powerfully, there was the conch. The being that had blown that, had sat waiting for them on the platform with the delicate thing balanced on his knees, was set apart.
It may have been more than just choosing the lesser of two evils, since the boys saw something in Ralph that inspired their vote. His bearing and his possession of the conch were the deciding factors.
You would think that Jack should be elected because he is head of the choir. But instead, Ralph is elected. I think this is because the boys have just made it to the island and are therefore still pretty civilized. Jack represents savagery and Ralph represents civilization.
You can sort of see this in the election scene. Jack is very aggressive. He is brutal to Piggy. He says that he should be the chief with "simple arrogance." He shows that he want power and he implies that he would be a mean leader.
I think this is why Ralph gets elected at first.