index.php in url for just channel pages I have followed the instructions for removing index.php and it works on all pages with the exception of pages with channels. So I would see http://www.example.com/index.php?p=news/2016/news-title.

I also added the 'omitScriptNameInUrls' =&gt; true, in the general.php file. 

Here is what I have in my .htaccess file

&lt;IfModule mod_rewrite.c&gt;
    RewriteEngine On

    # Send would-be 404 requests to Craft
    RewriteCond %{REQUEST_FILENAME} !-f
    RewriteCond %{REQUEST_FILENAME} !-d
    RewriteCond %{REQUEST_URI} !^/(favicon\.ico|apple-touch-icon.*\.png)$ [NC]
    RewriteRule (.+) index.php?p=$1 [QSA,L]
&lt;/IfModule&gt;

&lt;IfModule mod_deflate.c&gt;
    AddOutputFilterByType DEFLATE text/text text/html text/plain text/xml text/css application/x-javascript application/javascript image/svg+xml
&lt;/IfModule&gt;

&lt;IfModule mod_headers.c&gt;
    &lt;FilesMatch "\.(eot|otf|tt[cf]|woff2?)$"&gt;
        Header set Access-Control-Allow-Origin "*"
    &lt;/FilesMatch&gt;
&lt;/IfModule&gt;

Options +FollowSymLinks
RewriteEngine on
RewriteCond %{HTTP_HOST} ^example.com [NC]
RewriteRule ^(.*)$ http://www.example.com/$1 [R=301,L]
So it turns out I needed to have the "Options +FollowSymLinks" block above the craft rewrite rule in my htaccess. See comments above.