So I have tried both versions of the .htaccess, the one that comes with it in project creation and the one in the documentation. I am currently using the one in the documentation:
Options +FollowSymLinks
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^ index.php [L]
I have my virtualhost set up like so:
<VirtualHost *:80>
ServerAdmin <my email>
ServerName projectflyer.<my domain>.com
DocumentRoot /var/www/html/projects/project-flyer/public
DirectoryIndex index.php
ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>
However when I go to projectflyer.mydomain.com/some/route I get back a 404. Any ideas? Yes I can go to the base url just fine.
I solved this by adding this to my virtualhost .conf file:
<Directory /path/to/your/install/public/>
Options Indexes FollowSymLinks
AllowOverride All
Require all granted
</Directory>
Thanks to http://laravel.io/forum/09-15-2015-removing-indexphp-from-url-laravel-5116 for the answer