The following .htaccess is required to get mod_rewrite to work as expected under godaddy:

# Options
Options -Multiviews
Options +FollowSymLinks

#Enable mod rewrite
RewriteEngine On

#the location of the root of your site
#if writing for subdirectories, you would enter /subdirectory
RewriteBase /

#Checks to see if the user is attempting to access a valid file,
#such as an image or css document, if this isn't true it sends the
#request to index.php
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d

#This last condition enables access to the images and css
#folders, and the robots.txt file
RewriteCond $1 !^(index\.php|images|robots\.txt|css)

RewriteRule ^(.*)$ index.php?/$1 [L]

(The above code was from a google search from someone using CI with the same issue)

vs. original:

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteRule ^(.*)$ index.php/$1 [L]
</IfModule>

I don’t know why one works, not the other, and I really don’t care.