While I agree with much that has been said, I think that appealing to cultural traditions also played a large role in why Tolkien made so many of his prominant characters tall (or taller than their peers). Not only do the characters literally stand head and shoulders above everybody, it fits cultural perceptions that we understand (on some level) about height.
Re. Napoleon: I hate to burst everybody's bubble, but Napoleon was not unduly short for his day. He was (according to his autopsy) 1.686 meters tall, which made him a little bit
taller than the average Frenchman of his time. The impression of his shortness probably stems from his continually being surrounded by the Guard (who were all over six feet tall) and their enormous bearskin shakos (which a certain regiment of somebody's acquaintance...ummm...borrowed after a certain event.
).
Clicky here.