Agree with catorghans comments about .htaccess for Drupal being special. I’ve always used a custom Drupal core upgrade script that prevents .htaccess being override. Do core updates using drush preserve the main .htaccess?
Allowing scripts to change the .htaccess file is pretty much the most annoying thing about Wordpress and it’s plugins. Luckily Drupal is much more aware of screwing with the .htaccess.