Since we launched Shield we opted to not touch core WordPress/hosting files, like .htaccess. This is why Shield is stable – unlike other plugins, it’s doesn’t use the .htaccess as a dumping ground for rules that break sites. The worst part is when these plugins are disabled, they leave behind all their rubbish.
But…
With some of the recent plugin developments, we’re moving towards a position of being able to provide such an option in a more reliable way. We have plans for this, but we want to get it right, so it’ll take time to build up to it.
Getting .htaccess modifications wrong will break a site and the majority of admins don’t know how to recover it and most plugins don’t factor this in.