
For starters, it's just not popular. Some people don't like the way it sounds. However, you can't deny it's played some pretty significant rolls, though not so many as of recently. I personally love the way it sounds and think it's pretty awesome as a lead instrument and without it blues wouldn't be any where near what it is now.
Here's some classic blues songs that the harmonica leads in
http://www.youtube.com/watch?v=ZAgP3229jho
http://www.youtube.com/watch?v=zFoMZX-gy2Y
It's in some pretty sick songs in cowboy bebop
http://www.youtube.com/watch?v=fcSuJi1b0OU
http://www.youtube.com/watch?v=O0JB4wxtSJk
How about another instrument? The fucking xylophone man this poor thing gets no recognition but it's pretty awesome.

Awww yeah, you remember me dog. How could you forget, you probably played with me a time or two when you were a child.
And guess what, it was fun as hell wasn't it? Yeah it was.
Try this xylophone solo with an orchestra backing it.
http://www.youtube.com/watch?v=VRAyL5ai5Lg
Plus they sound unique and play an important roll in a symphony.
Try this more new age, quirky song.
http://www.youtube.com/watch?v=yzfzsKENCbU
lol
This songs insane, man.
http://www.youtube.com/watch?v=KPHdNcK4jCc&feature=related
Your turn guys, what do you know people don't appreciate?