wordpress htaccess redirected www to folder

Solution:

Keep redirect rule at top and make it target only main domain:

RewriteEngine On
RewriteBase /

RewriteCond %{HTTP_HOST} ^main\.com$ [NC]
#RewriteRule ^ http://www.%{HTTP_HOST}%{REQUEST_URI} [R=301,L,NE]
RewriteRule ^ http://%{HTTP_HOST}%{REQUEST_URI} [R=301,L,NE]

RewriteRule ^index\.php$ - [L]

RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . index.php [L]

Make sure to clear your browser cache before testing this change.

Edit:

Removing the www in the RewriteRule has solved the issue.