I am also having the same problem and I have tried almost every code available online for .htaccess
My Xamp is running on Linux, FYI - The application is on intranet not on internet, may be that cause some problem.
I have checked that mod_rewrite is enabled. it is showing under loaded modules when I run php.info() function.
In my config file
$config['base_url'] = '';
$config['index_page'] = '';
$config['uri_protocol' = 'AUTO';
my working url is arteri is a subdirectory in root http://whintranet.wh.tvh.ca/arteri/index.php/artery/home but when I removes index.php from it
The requested URL /arteri/artery/home was not found on this server. Apache/2.2.15 (CentOS) Server at whintranet.wh.tvh.ca Port 80
my.htaccess
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /arteri/
RewriteCond %{REQUEST_URI} ^system.*
RewriteRule ^(.*)$ /index.php?/$1 [L]
RewriteCond %{REQUEST_URI} ^application.*
RewriteRule ^(.*)$ /index.php?/$1 [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]
</IfModule>
any help greately appreciated