Is there a way to keep people from downloading cerain files on a server?
 

I have some javascript functions that I think others will steal. How do I protect them?

Theyre in a seperate file on my server, they're not on the page, but they're referenced on the page and easy to locate and download.

will .htaccess keep these files from being downloadable?

Post them here with a note that says "DO NOT STEAL." That will keep them safe.