The problem occurs when you have a lot of sites, and do not want *anyone* to
run PHP. You have to disable not only the PHP input. But also the ability
for people to switch it on. Which means you ghave to seriously restrict all
their permissions.
Same goes for when you *do* what Joe Moderator of your site to be able to
administer certain areas (like users) but definately not to give the the
option to run code.