Because by design, whatever you didn't get from iTunes won't carry over.
Now you can either get one of the programs Macroplant offers, which will help you carry over not just music but movies, books, and everything else (including game saves), or you can choose to restore your music library from elsewhere.
Either way, you have to get files back into your iTunes library before you can put them on the iPad. Common sense is to backup iTunes before reformat, but I'm supposing this is your first time.
Here's a link to Macroplant:
http://macroplant.com/index.php