var myDocument = app.documents.item(0);
//Get a reference to the text frame.
var myTextFrame = textFrames.item(0);
var myParagraph = myTextFrame.paragraphs.item(0);
myHyperlinkURL = myDocument.hyperlinkURLDestinations.add("http://www.publishingsilicon.com");
myHyperlinkSource = myDocument.hyperlinkTextSources.add(myParagraph);
myHyperlink = myDocument.hyperlinks.add(myHyperlinkSource,myHyperlinkURL);
This assumes a text frame exists with some text in it, and that when you export the PDF you either check Include\hyperlinks in the PDF Export dialogue, or do the equivalent with code if exporting programmatically.
I need to get around to updating that data-generated example some day. Amazing how many people around the world seem to stumble upon it.