.htaccess not affecting other folders

I have a .htaccess file that affects my subdomains folder, how do I prevent that f开发者_开发技巧rom happening. Want the subdomain to run independent of the .htaccess file. Here is my .htaccess code

RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^([a-zA-Z]*)/?$ goto.php?page=$1
ErrorDocument 404 PageNotFound
IndexIgnore *

####Protect the system from machines with worms 
RewriteRule (cmd|root)\.exe - [F,E=dontlog:1]

##Search Business
RewriteRule %{QUERY_STRING} search.php?id=$1

RewriteRule ^Customise/([0-9]*)/([A-Za-z-]*)$ customise.php?id=$1

#### To hold and redirect css/images/js files
RewriteRule images/(.+)?$ images/$1 [NC,L]
RewriteRule css/(.+)?$ css/$1 [NC,L]
RewriteRule js/(.+)?$ js/$1 [NC,L]
RewriteRule uploads/(.+)?$ uploads/$1 [NC,L]

Set AllowOverride option to None in httpd-conf for your subdomains directories (see Apache docs).