.htaccess should be
<IfModule mod_rewrite.c>
Options -MultiViews
RewriteEngine On
RewriteBase /web/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^ index.php [QSA,L]
</IfModule>
VirtualHost file must looks like this
<VirtualHost *:80>
ServerName site.com
ServerAlias www.site.com
DocumentRoot /var/www/html/silex/
ErrorLog ${APACHE_LOG_DIR}/error.log
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>
And everithing works like a charm! ;-)
".htaccess" located at /var/www/html/silex/
and Silex application bundle
placed at /var/www/html/silex/web/