How to take care of .htaccess of all sites in multi-site setup on Linux? I've read this article: http://drupal.org/node/290768 which explains multisite settings on Linux.

But I need separate .htaccess for each site. How do I do it?
You cannot have separate .htaccess files in Drupal's root directory.  

You can have different rewrite condition inside your Drupal's root .htaccess file .

You can have separate .htaccess inside your sites/%mysite%/ directory which will control all the files, modules, themes, etc related to that specific site.