Deny all files in a certain directory using <files>

Maybe your problem is in the FilesMatch directive; FilesMatch uses regex to match directives, therefore, to obtain what you want, you should write:

<FilesMatch "/home/.*/domains/.*/.*">
    Order deny,allow
    Deny from all
</FilesMatch>

I don't believe you can specify a path in any of the Files directives. And also it doesn't look like you really need the FilesMatch directive, as you aren't really using any complex pattern to require regex's. I usually put my Files directives inside the directory though to make it simple.

This seemed to work for me with a setup similar to yours. Under /var/www/domains there is 1/ 2/ and 3/ each with various html files. None are accessible now.

<Directory /var/www/domains/*/>
        Options None
        AllowOverride None
        Order Allow,Deny
        Deny from All
        <Files *>
                Order Allow,Deny
                Deny from All
        </Files>
</Directory>