Do this, This line helps me solve the issue.
<pre>
# .htaccess main domain to subdirectory redirect # Do not change this line. RewriteEngine on # Change example.com to be your main domain. RewriteCond %{HTTP_HOST} ^(www.)?example.com$ # Change 'subdirectory' to be the directory you will use for your main domain. RewriteCond %{REQUEST_URI} !^/subdirectory/ # Don't change the following two lines. RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d # Change 'subdirectory' to be the directory you will use for your main domain. RewriteRule ^(.*)$ /subdirectory/$1 # Change example.com to be your main domain again. # Change 'subdirectory' to be the directory you will use for your main domain # followed by / then the main file for your site, index.php, index.html, etc. RewriteCond %{HTTP_HOST} ^(www.)?example.com$ RewriteRule ^(/)?$ subdirectory/index.html [L]
</pre>

I have it organized the same way yo do. Had the same issue with my main domain. This .htaccess works for me and even solves the ugly URL thing.
# .htaccess main domain to subdirectory redirect RewriteEngine on # Change example.com to be your main domain. RewriteCond %{HTTP_HOST} ^(www.)?example.com$ # Change 'subdirectory' to be the directory you will use for your main domain. RewriteCond %{REQUEST_URI} !^/subdirectory/ # Don't change the following two lines. RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d # Change 'subdirectory' to be the directory you will use for your main domain. RewriteRule ^(.*)$ /subdirectory/$1 # Change example.com to be your main domain again. # Change 'subdirectory' to be the directory you will use for your main domain # followed by / then the main file for your site, index.php, index.html, etc. RewriteCond %{HTTP_HOST} ^(www.)?example.com$ RewriteRule ^(/)?$ subdirectory/ [L]