Below is the command I tried executing, without success:
exec('ln -s ' . PLUGIN_DIR . '/.htaccess ' . ABSPATH . '/.htaccess');
When you add a die() at the end, it catches that there's an error:
exec('ln -s ' . PLUGIN_DIR . '/.htaccess ' . ABSPATH . '/.htaccess') or die('what?!');
For the above exec() statement, a permissions problem is causing the error, but PHP isn't displaying it. How do you display from PHP what error is occurring?