how is it ironic that the boys killed simon ?

Simon was more than just a sensitive boy. By the end of the novel he becomes Golding's Christ-figure. That is he has the personality characteristics of a messiah/saviour sort of person. Simon knew the truth both literally and metaphorically. He saw the only evil on the island was inside the boys themselves. When Simon sees the dead pilot he knew that, on a literal sense, he was the creature the boys mistook for the beast. As Simon crawled out of the jungle to proclaim the "good news", he is mistaken for the beast and killed. The irony is that their saviour is thought of as their enemy, much like Christ in the New Testament. They also violently kill the most gentle boy on the island.