Rules from the root are applied to subdirectories ONLY if those subdirectories are void of their own htaccess.
Awk. Someone, somewhere, is interpreting that to mean that if you have
/directory with htaccess
/directory/subdirectory1 with htaccess
/directory/subdirectory2 without htaccess
then requests for material in /subdirectory1 will ignore
everything in the higher-level /directory/ htaccess. And I'm morally certain that's not what you meant.
Simplest case: the htaccess file that people will have even if they are deathly afraid of htaccess.
config file (which you can't touch) says "Options +Indexes"
>> all directories everywhere on the server use auto-indexing
/directory/ htaccess says "Options -Indexes"
>> everything in /directory/
and its descendants will have auto-indexing
off /directory/subdirectory1 htaccess says "Options +Indexes"
/directory/subdirectory2 htaccess says nothing about Indexes
/directory/subdirectory3 has no htaccess
>> /subdirectory1
and its descendants will have auto-indexing
on. /subdirectories 2 and 3 will continue to have it
off. And you can keep toggling this setting, level by level.
Basic rule: Anything said explicitly in a higher-level directory will apply to all descendants of that directory-- with a few exceptions.
One exception that you've probably met: If an htaccess file uses mod_rewrite, it has to contain the line "RewriteEngine On". It doesn't simply get turned on and then stay on for all subdirectories.
If you're on shared hosting, not all directives can go in all places. For example: I have two domains sharing a userspace. I can have a lot of stuff in a shared htaccess, including core "Deny From..." directives. But I can't put the "Options -Indexes" directive up there. It won't make the site crash; it will simply be ignored. (I know this by direct experiment. It is probably not universally true of all shared-hosting setups.)