CNN's Vatican analyst John Allen says that like so much concerning religion, the belief that the bones are those of the disciple comes down to faith.
"Like other famous relics, such as the Shroud of Turin or the Belt of Mary, they evoke awe and devotion regardless of their actual provenance," Allen writes in an Op-Ed for CNN. "Faith, as the Bible puts it, lies in 'the evidence of things not seen.'"
MORE: http://www.cnn.com/2013/11/22/world/europe/st-peters-bones-on-display/index.html