I've moved your question to the InDesign EPUB forum.
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Is your EPUB 3 file set for Reflowable EPUB or Fixed Layout EPUB? I suspect the latter.
If so, you've run into a current limitation of EPUB 3 Fixed Layout. It doesn't yet support text hyperlinks. Only object hyperlinks. This will probably be fixed in the next InDesign CC 2014 update.
Anne-Marie Conception suggested a workaround (probably a bit of a pain). You can create a graphic frame and place a picture in it (required). Then set the opacity of the picture to 0%. Place the graphic frame on a separate layer above the text you want to link. Create a hyperlink to that frame. She mentioned this in the most recent podcast on www.indesignsecrets.com.