The main domain on the hosting account uses the public_html directory for all of its Web site files. Addon domains use sub directories inside the public_html directory. In order to also set up your main domain to use a subdirectory on your hosting account you will need to set up a redirect in the .htaccess file in the public_html folder so that the server knows that any request for your main domain will be redirected to a subdirectory on public_html.
To setup the rewrite/redirect, edit the ~/public_html/.htaccess file. Insert the following code block and make modifications as noted in the (#) comments.
# Bluehost.com
# .htaccess main domain to subdirectory redirect
# Copy and paste the following code into the .htaccess file
# in the public_html folder of your hosting account
# make the changes to the file according to the instructions.
# Do not change this line.
RewriteEngine on
# Change yourdomain.com to be your main domain.
RewriteCond %{HTTP_HOST} ^(www.)?yourmaindomain.com$
# Change ‘subdirectory’ to be the directory you will use for your main domain.
RewriteCond %{REQUEST_URI} !^/subdirectory/
# Don’t change this line.
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
# Change ‘subdirectory’ to be the directory you will use for your main domain.
RewriteRule ^(.*)$ /subdirectory/$1
# Change yourdomain.com to be your main domain again.
# Change ‘subdirectory’ to be the directory you will use for your main domain
# followed by / then the main file for your site, index.php, index.html, etc.
RewriteCond %{HTTP_HOST} ^(www.)?yourmaindomain.com$
RewriteRule ^(/)?$ subdirectory/index.php [L]