I would recommend trying to add

DirectoryIndex index.php index.html

and restarting apache with

service apache2 restart

This will direct apache to use your index.php file rather than showing a directory index.

@blakeingram405

Try running the command below and post the output.

apachectl configtest

Beyond that, Apache can be finicky at times, so you may want to try defining the DocumentRoot at the top, so your configuration would end up looking like:

<VirtualHost *:443>
DocumentRoot "/var/www/html"
ServerName prollagen.com
ServerAlias *.prollagen.com
SSLEngine On
SSLCertificateFile /etc/ssl/key
SSLCertificateKeyFile /etc/ssl/key
SSLCertificateChainFile /etc/ssl/key

<Directory /var/www/html/>
    Options Indexes FollowSymLinks
    AllowOverride All
    Require all granted
</Directory>

ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>

Note, I added a ServerAlias line below ServerName to allow other requests to resolve to the primary domain. You should also setup a similar block to allow requests on port 80 as well.

Using the above, you're essentially telling Apache to listen on Port 443 only.

@blakeingram405

As a word of advice, by using Options Indexes instead of Options -Indexes, you're enabling all directories, starting at /var/www/html and including anything below it, to be openly browsed by anyone who can access them unless every single one of them has its own index file.

For example, let's say you have:

/var/www/html/example
/var/www/html/example/config.php
/var/www/html/example/passwords.php
/var/www/html/example/....

With Options Indexes, I can browse to yourdomain.ext/example and take a look at those files. If they just so happen to output data (whether intentional or perhaps there's an issue with your PHP configuration that lets me download the files or access them in another way), I might just be able to access whatever it is you're trying to protect or keep private. If that happens to give me access to your database, backend, web server, etc -- you may find yourself in a less than desirable position.

Even if I didn't know your directory structure, I could run a few thousand basic requests, each of which would attempt to guess at directory structure using a dictionary or similar. If I happen to see that one of them works and returns an index listing of files, they will be scanned for something useful.

To prevent this, you'd need to drop an index.html file in that directory and any other directory that doesn't have one, starting from /var/www/html.

Unless you have a specific reason to allow open browsing, I'd use Options -Indexes, that way you don't have to worry about whether and index file exists or not.

So cloudflare was the problem!
As with "Options -Indexes", when placing - in front of indexes apache throws out an error stating "if an option has - or +, all other options must have the same"

What would another "option" be within 000-default?