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I had the same problem with a Wildcard SSL certificate and Bluehost. I emailed support so that I could get to a Level II support person and here is the response I got. This solved the problem.

The problem with running wordpress and a wildcard certificate at the same time is that both of them have their own special .htaccess mod_rewrite rules. You can’t just use both sets of rules together, it must be a hybrid of the rules to work properly.

Luckily I have come across this specific situation before and so I know the rules you’ll need. Your .htaccess has been changed to the following:

# Use PHP5 as default
AddHandler application/x-httpd-php5 .php

# wordpress rules for maindomain.com site
RewriteEngine On
RewriteBase /
RewriteCond %{HTTP_HOST} ^(www\.)?maindomain.com$
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]

# wordpress rules for subdomain.maindomain.com site
RewriteEngine On
RewriteCond %{HTTP_HOST} ^subdomain.maindomain.com$
RewriteCond %{REQUEST_URI} !^/subdomain-folder-name-here/
RewriteRule ^(.*)$ /subdomain-folder-name-here/$1
RewriteCond %{HTTP_HOST} ^subdomain.maindomain.com$
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(/)?$ subdomain-folder-name-here/index.php [L]