As Steve mentions, you do need to enable FileMaker APIs for PHP and XML in the CLI as follows:
PHP and XML web publishing settings
When you configure web publishing settings, Admin Console restarts the Web Publishing Engine. During this time, all web published databases are unavailable to web users.
Important Change web publishing settings only when the Web Publishing Engine is not being used. Web publishing clients can lose unsaved work when the Web Publishing Engine restarts.
To enable the FileMaker API for PHP, use the CLI command:
fmsadmin set cwpconfig enablephp=true
To enable the FileMaker API for XML, use the CLI command:
fmsadmin set cwpconfig enablexml=true
See Using the command line interface.
For information about using the FileMaker API for PHP and the FileMaker API for XML, see FileMaker Server Custom Web Publishing Guide.
Notes
•If you enable Custom Web Publishing, import a custom SSL certificate to use SSL data encryption when transmitting data. See Importing a custom SSL certificate.
•The FileMaker API for PHP and a supported PHP engine must be installed on the master machine for Custom Web Publishing with PHP to work. See FileMaker Server Custom Web Publishing Guide.
•The FileMaker API for XML must be enabled on the master machine for Custom Web Publishing with XML to work. See FileMaker Server Custom Web Publishing Guide.
•For information about hosting a PHP website, see Hosting websites.