.htaccess not working with SSL config - apache

Question

I followed this guide to get a free SSL certificate from StartSSL: https://www.digitalocean.com/community/tutorials/how-to-set-up-apache-with-a-free-signed-ssl-certificate-on-a-vps
I followed it step by step but I don't actually understand it fully as I'm a newbie.
I have .htaccess which stopped working after I put the below code into my 000-default.conf file:
<VirtualHost *:443>
SSLEngine on
SSLProtocol all -SSLv2
SSLCipherSuite ALL:!ADH:!EXPORT:!SSLv2:RC4+RSA:+HIGH:+MEDIUM
SSLCertificateFile /etc/apache2/ssl/ssl.crt
SSLCertificateKeyFile /etc/apache2/ssl/private.key
SSLCertificateChainFile /etc/apache2/ssl/sub.class1.server.ca.pem
ServerAdmin webmaster#localhost
DocumentRoot /var/www/html
<Directory />
Options FollowSymLinks
AllowOverride None
</Directory>
<Directory /var/www/html>
Options Indexes FollowSymLinks MultiViews
AllowOverride None
Order allow,deny
allow from all
</Directory>
ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/
<Directory "/usr/lib/cgi-bin">
AllowOverride None
Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch
Order allow,deny
Allow from all
</Directory>
ErrorLog ${APACHE_LOG_DIR}/error.log
# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn
CustomLog ${APACHE_LOG_DIR}/access.log combined
Alias /doc/ "/usr/share/doc/"
<Directory "/usr/share/doc/">
Options Indexes MultiViews FollowSymLinks
AllowOverride None
Order deny,allow
Deny from all
Allow from 127.0.0.0/255.0.0.0 ::1/128
</Directory>
</VirtualHost>
This is what's in my .htaccess file:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^([a-zA-Z0-9\-]+)$ $1.php
ErrorDocument 404 /404error
</IfModule>
^ It's basically to be able to access a page like this domain/page rather than like this: domain/page.php
So as soon as I add the above code from the 000-default.conf file, the rewrite rule works fine. If I add it in, however, I can no longer access files without the .php at the end. My 404 redirect is also not working.
What is it that's causing the problem?