Several reasons:

* The bindings for making anything GUI-ish lack. Horribly. I doubt there is one application like an editor written in PHP; that is actually used. * Its long-threads are ... lacking; You cannot write anything deamon-ish in PHP. * Memory management, as Ramus puts it, is not a concern "I just restart Apache". That makes it unusable for anything bigger then a small CLI-tool. * The Cli-libraries are decent, but far from things like Ruby's Thor.

You can write CLI-tools just fine, but "general purpose" is much more then "Managing Web-Content And Some CLI tools".