If there is a way to use .htaccess to count downloads then I don't know it. I'd be happy to hear of one though.
I use PHP for several reasons. It makes a good counting system, especially when combined with an underlying MySQL database, and also (very important) it hides the actual URL of the downloaded file.
Try any one of dozens of possible scripts from Hotscripts:
This one is pretty good:
The site statistics provided by your web host can also tell you how many downloads have been requested.