This is how we solved this problem: adding a condition to ignore the rewrite if requesting from the assets folder. You can add/remove options to ignore as required - really you only need the assets option in your case.
#Checks to see if the user is attempting to access a valid file,
#such as an image or css document
RewriteCond $1 !^(index\.php|assets|css|png|jpg|gif|robots\.txt|favicon\.ico)
Place this before your RewriteRule.
There's a pretty comprehensive Codeigniter .htaccess for troublesome hosts at: http://www.chrishjorth.com/blog/one-com-codeigniter-htaccess-rewrite-rules/, that's nicely commented:
# @author: Chris Hjorth, www.chrishjorth.com
# Make index.php the directory index page
DirectoryIndex index.php
#Protect the .htaccess files
<Files .htaccess>
order allow,deny
deny from all
</Files>
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /subfolder/
# START CodeIgniter ------------------------------------------------------------------------------------------------------------
# based on http://www.danielwmoore.com/extras/index.php?topic=7691.0 and http://ellislab.com/forums/viewthread/132758/
# Redirect default controller to "/".
# This is to prevent duplicated content. (/welcome/index => /)
RewriteRule ^(welcome(/index)?)/?$ /subfolder/ [L,R=301]
# Remove /index/ segment on the URL, again to prevent duplicate content.
RewriteRule ^(.*)/index/? $1 [L,R=301]
# Remove trailing slashes, also to remove duplicate content
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# Remove multiple slashes in between, just to remove the possibility of fabricating crazy links.
RewriteCond %{REQUEST_URI} ^(.*)//(.*)$
RewriteRule . %1/%2 [R=301,L]
# Ignore certain files and folders in this rewrite
RewriteCond $1 !^(index\.php|assets|frameworks|uploads|robots\.txt|favicon\.ico)
# [NC] = no case - case insensitive
# [L] = Last rule, last rewrite for this set of conditions
# [QSA] = Query String Append, should be used to prevent all redirects from going to your default controller, which happens on
# some server configurations.
RewriteRule ^(.*)$ /subfolder/index.php?$1 [NC,L,QSA]
# END CodeIgniter --------------------------------------------------------------------------------------------------------------
</IfModule>
# If Mod_rewrite is NOT installed go to index.php
<IfModule !mod_rewrite.c>
ErrorDocument 404 /index.php
</IfModule>