Okay so after hitting hammer in my head, I found working properly. However I am not so sure if I have done correctly or there is any better approach to make it works.
What I have done first is,
Change permission for entire /var/www
again. I just wonder, why I have to reset it after pasting the site, I have done that before.
sudo chmod -R 775 /var/www
You may like to change group or owner etc..(also let me know if any good way to assign owner or group)
Than, I have added rewrite rule as below in..
sudo gedit /etc/apache2/sites-available/000-default.conf
Add below to 000-default.conf
<Directory /var/www/html>
AllowOverride All
</Directory>
I checked and now everything is working fine.
Please, correct me or guide me if there is any better approach. I have just search here in some answers and apply simple logic to fix it. I am newbie and not good in all these.