You need to add the following line into each .htaccess in subfolders if you want to have rewrite rules from parent .htaccess to be executed as well:

RewriteOptions inherit

This forces the current configuration to inherit the configuration of the parent. In per-virtual-server context, this means that the maps, conditions and rules of the main server are inherited. In per-directory context this means that conditions and rules of the parent directory's .htaccess configuration are inherited.

Rules inherited from the parent scope are applied after rules specified in the child scope.

http://httpd.apache.org/docs/current/mod/mod_rewrite.html#rewriteoptions

from
http://stackoverflow.com/questions/7443902/get-htaccess-from-root-directory-to-apply-on-all-directories