So, the reason Harry says he isn't afraid to call Voldemort by his name is because he was never brought up to, right? I think the quote is something like "I didn't know I was supposed to be afraid of the name." But I think it has to be more than that. Because Hermione has only read about how awful it was, and she can't say it (which I think is a crazy interesting statement to the power of books and how important they are to her), and beyond her, there are tons of other Muggle-borns in the school/Wizarding world at large who won't say his name. I think it must have to do with Harry's general awesomeoness, lack of fear in general, respect for Dumbledore and everything he says, or connection to Voldemort.