Disable plugin for subdomain

Yes. You are correct. The parent htaccess file in the hosting account root folder will apply its htaccess rules to all child folders by default since that is the natural hierarchical/recursive nature of htaccess files.

This forum topic explains this in full detail: http://forum.ait-pro.com/forums/topic/htaccess-files-for-multiple-website-domains/

Basically what you want to do is this (using subdomainA as an example subdomain folder name for this example):
Using BPS Custom Code you want to copy the WP REWRITE LOOP START htaccess code from your root htaccess file into this BPS Root Custom Code text box: CUSTOM CODE WP REWRITE LOOP START.
Edit the code and add the additional RewriteRule for sudomainA (you would use your actual subdomain folder name).
Click the Save Root Custom Code button.
Go to the BPS Security Modes page, click the Create secure.htaccess File AutoMagic button and activate Root folder BulletProof Mode.

# WP REWRITE LOOP START
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]

# Do not apply rules to other child websites &
# do not log errors for these child sites
RewriteRule ^subdomainA/ - [L]