What makes Ruby, Python and Perl more secure than PHP?
The fact that those languages don't have "magic_quotes" or "globals_on"?
For more than 3 year I've not seen "magic_quotes" or "globals_on" turned on anywhere. As far as I know in php6 there won't be globals option at all.
Neither have I. If you care one bit about security, that's the first thing you'll find out about PHP and as you said, they are being eliminated from the php.ini file in php6 and will need to explicitely turned on in your scripts.
PHP is popular because of how easy it was to get started and how available it was in every dirt cheap shared hosting plan on the market. Sure, it's not the most elegant language and it does have plenty of issues but quite a few of these are solved with quality planning and the use of quality tools such as CodeIgnitor or CakePHP.
The low barriers to entry are what made PHP popular and the fact that you can code something robust and maintainable are allowing it to sustain.