404 permalink problem – I did everything I could

Hi,

I have installed wordpress several times before but I could not fix 404 error on my permalink this time. :S I tried everything I could search to fix it but I still need some help!

Environment:
Ubuntu 14.04

My wordpress files are located in a virtual host folder
/home/site.com/www

in apache2.conf

<Directory />
	Options FollowSymLinks
	AllowOverride None
	Require all denied
</Directory>

<Directory /usr/share>
	AllowOverride None
	Require all granted
</Directory>

<Directory /var/www/>
	Options Indexes FollowSymLinks
	AllowOverride None
	Require all granted
</Directory>

in site.com.config

<VirtualHost *:80>
DocumentRoot "/home/site.com/www"
ServerName www.site.com
<Directory "/home/site.com/www">
allow from all
Options None
Require all granted
</Directory>
</VirtualHost>

in .htaccess

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

rewrite mod is running
and apache2 was restarted.

But the browser still shows 404 error..

Please give me some tips!!