How to configure htaccess to work on subdirectory?

Question

I have two website structure with 2 .htaccess like this:

www > html> .htaccess
www > vhosts > www.website2.com > http > .htaccess

both have this code inside

Options +FollowSymLinks +ExecCGI

<IfModule mod_rewrite.c>
  RewriteEngine On

 # Reroute to index.php
  RewriteCond $1 !^(index\.php)
  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteRule ^(.*)$ index.php [L,QSA]

</IfModule>

This allows me to avoid putting index.php in URLs like:

http://localhost/website1.com/html/index.php/es_ES/hotels

can be used as:

http://localhost/website1.com/html/es_ES/hotels

but in the second website if I don't use index.php isn't working.

What's wrong?